Como multiplexar dois vídeos com ffmpeg

Estou convertendo vídeos usando a opção -s para várias resoluções e quero incluir uma breve introdução no início do vídeo. mas, por algum motivo, pula o segundo, -ientão eu só estou recebendo a introdução Opener_4.mp4sem o vídeo hdvd.mkv.

O que eu tentei: (* eu tentei com e sem a opção de mapa)

ffmpeg -i Opener_4.mp4 -i hdvd.mkv -map 0:0 -map 0:1  
  -s 1836x1080 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_1080p.mp4 
  -s 1224x720 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_720p.mp4 
  -s 816x480 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_480p.mp4 
  -s 612x360 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_360p.mp4 
  -s 408x240 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_240p.mp4 
  -s 244x144 -map 0:0 -map 0:1 -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_144p.mp4

o registro

ffmpeg version 1.2.3 Copyright (c) 2000-2013 the FFmpeg developers
  built on Sep  5 2013 03:04:34 with gcc 4.7 (Debian 4.7.1-2)
  configuration: --enable-gpl --enable-libass --enable-libfaac --enable-libfdk-aac --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libspeex --enable-librtmp --enable-libtheora --enable-libvorbis --enable-libvpx --enable-x11grab --enable-libx264 --enable-nonfree --enable-version3
  libavutil      52. 18.100 / 52. 18.100
  libavcodec     54. 92.100 / 54. 92.100
  libavformat    54. 63.104 / 54. 63.104
  libavdevice    54.  3.103 / 54.  3.103
  libavfilter     3. 42.103 /  3. 42.103
  libswscale      2.  2.100 /  2.  2.100
  libswresample   0. 17.102 /  0. 17.102
  libpostproc    52.  2.100 / 52.  2.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'Opener_4.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    creation_time   : 2013-03-03 06:57:29
  Duration: 00:00:13.35, start: 0.000000, bitrate: 6744 kb/s
    Stream #0:0(eng): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 6611 kb/s, 29.97 fps, 29.97 tbr, 30k tbn, 59.94 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #0:1(eng): Audio: aac (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 125 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Input #1, matroska,webm, from 'hdvd2.mkv':
  Metadata:
    creation_time   : 2007-04-07 03:28:47
  Duration: 00:02:01.90, start: 0.000000, bitrate: 19153 kb/s
    Stream #1:0(eng): Video: vc1 (Advanced) (WVC1 / 0x31435657), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 29.97 tbr, 1k tbn, 59.94 tbc (default)
    Metadata:
      title           : 1080p VC-1
    Stream #1:1(eng): Audio: ac3, 48000 Hz, stereo, fltp, 640 kb/s (default)
    Metadata:
      title           : Dolby Digital 2.0 640kbps
    Stream #1:2(eng): Audio: eac3, 48000 Hz, 5.1(side), fltp, 640 kb/s
    Metadata:
      title           : Dolby Digital Plus 5.1 640kbps
[libx264 @ 0x2df64c0] using SAR=160/153
[libx264 @ 0x2df64c0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2df64c0] profile High, level 4.0
[libx264 @ 0x2df64c0] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=8 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2d8dd80] using SAR=160/153
[libx264 @ 0x2d8dd80] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2d8dd80] profile High, level 3.1
[libx264 @ 0x2d8dd80] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=8 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2de9c00] using SAR=160/153
[libx264 @ 0x2de9c00] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2de9c00] profile High, level 3.1
[libx264 @ 0x2de9c00] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=7 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2dee860] using SAR=160/153
[libx264 @ 0x2dee860] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2dee860] profile High, level 3.0
[libx264 @ 0x2dee860] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=5 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2df1400] using SAR=160/153
[libx264 @ 0x2df1400] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2df1400] profile High, level 1.3
[libx264 @ 0x2df1400] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=3 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2dcf1e0] using SAR=64/61
[libx264 @ 0x2dcf1e0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2dcf1e0] profile High, level 1.2
[libx264 @ 0x2dcf1e0] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=2 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'hdvd2.mkv_1080p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #0:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1836x1080 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #0:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #1, mp4, to 'hdvd2.mkv_720p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #1:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1224x720 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #1:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #2, mp4, to 'hdvd2.mkv_480p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #2:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 816x480 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #2:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #3, mp4, to 'hdvd2.mkv_360p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #3:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 612x360 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #3:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #4, mp4, to 'hdvd2.mkv_240p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #4:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 408x240 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #4:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #5, mp4, to 'hdvd2.mkv_144p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #5:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 244x144 [SAR 64:61 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #5:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Stream mapping:
  Stream #0:0 -> #0:0 (h264 -> libx264)
  Stream #0:1 -> #0:1 (aac -> aac)
  Stream #0:0 -> #1:0 (h264 -> libx264)
  Stream #0:1 -> #1:1 (aac -> aac)
  Stream #0:0 -> #2:0 (h264 -> libx264)
  Stream #0:1 -> #2:1 (aac -> aac)
  Stream #0:0 -> #3:0 (h264 -> libx264)
  Stream #0:1 -> #3:1 (aac -> aac)
  Stream #0:0 -> #4:0 (h264 -> libx264)
  Stream #0:1 -> #4:1 (aac -> aac)
  Stream #0:0 -> #5:0 (h264 -> libx264)
  Stream #0:1 -> #5:1 (aac -> aac)
Press [q] to stop, [?] for help
Starting second pass: moving header on top of the file q=29.0 size=    3630kB time=00:00:13.31 bitrate=2233.6kbits/s dup=6 drop=0    
[mp4 @ 0x2d8d4e0] Starting second pass: moving header on top of the file
[mp4 @ 0x2de9360] Starting second pass: moving header on top of the file
[mp4 @ 0x2dedec0] Starting second pass: moving header on top of the file
[mp4 @ 0x2df0ba0] Starting second pass: moving header on top of the file
[mp4 @ 0x2dcea60] Starting second pass: moving header on top of the file
frame=  401 fps= 12 q=-1.0 Lq=-1.0 q=-1.0 q=-1.0 q=-1.0 q=-1.0 size=    4548kB time=00:00:13.35 bitrate=2789.7kbits/s dup=6 drop=0    
video:8523kB audio:1165kB subtitle:0 global headers:0kB muxing overhead -53.057493%
[libx264 @ 0x2df64c0] frame I:3     Avg QP:17.44  size: 42261
[libx264 @ 0x2df64c0] frame P:166   Avg QP:22.23  size: 18663
[libx264 @ 0x2df64c0] frame B:232   Avg QP:25.06  size:  5246
[libx264 @ 0x2df64c0] consecutive B-frames: 16.0% 17.5%  9.7% 56.9%
[libx264 @ 0x2df64c0] mb I  I16..4: 55.8% 38.3%  6.0%
[libx264 @ 0x2df64c0] mb P  I16..4: 13.8% 10.0%  0.5%  P16..4: 40.1%  5.7%  2.9%  0.0%  0.0%    skip:26.9%
[libx264 @ 0x2df64c0] mb B  I16..4:  0.4%  0.2%  0.0%  B16..8: 31.4%  1.7%  0.2%  direct: 1.4%  skip:64.7%  L0:39.9% L1:56.8% BI: 3.3%
[libx264 @ 0x2df64c0] 8x8 transform intra:40.7% inter:82.6%
[libx264 @ 0x2df64c0] coded y,uvDC,uvAC intra: 16.4% 37.0% 3.3% inter: 6.3% 16.0% 0.1%
[libx264 @ 0x2df64c0] i16 v,h,dc,p: 37% 26%  7% 30%
[libx264 @ 0x2df64c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 26% 21% 34%  3%  4%  4%  3%  3%  3%
[libx264 @ 0x2df64c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 17% 41%  4%  5%  4%  3%  3%  2%
[libx264 @ 0x2df64c0] i8c dc,h,v,p: 61% 21% 14%  3%
[libx264 @ 0x2df64c0] Weighted P-Frames: Y:31.3% UV:29.5%
[libx264 @ 0x2df64c0] ref P L0: 71.5%  8.9% 15.0%  4.5%  0.0%
[libx264 @ 0x2df64c0] ref B L0: 90.9%  7.7%  1.5%
[libx264 @ 0x2df64c0] ref B L1: 95.8%  4.2%
[libx264 @ 0x2df64c0] kb/s:2655.87
[libx264 @ 0x2d8dd80] frame I:3     Avg QP:17.88  size: 25469
[libx264 @ 0x2d8dd80] frame P:141   Avg QP:22.69  size:  9944
[libx264 @ 0x2d8dd80] frame B:257   Avg QP:25.83  size:  2403
[libx264 @ 0x2d8dd80] consecutive B-frames: 11.5%  8.0%  3.7% 76.8%
[libx264 @ 0x2d8dd80] mb I  I16..4: 48.3% 42.9%  8.8%
[libx264 @ 0x2d8dd80] mb P  I16..4:  8.8%  9.5%  0.6%  P16..4: 42.2%  8.5%  4.2%  0.0%  0.0%    skip:26.1%
[libx264 @ 0x2d8dd80] mb B  I16..4:  0.2%  0.1%  0.0%  B16..8: 30.2%  2.4%  0.4%  direct: 1.8%  skip:64.8%  L0:38.7% L1:55.8% BI: 5.5%
[libx264 @ 0x2d8dd80] 8x8 transform intra:49.2% inter:74.2%
[libx264 @ 0x2d8dd80] coded y,uvDC,uvAC intra: 23.3% 39.3% 4.8% inter: 6.7% 12.8% 0.2%
[libx264 @ 0x2d8dd80] i16 v,h,dc,p: 38% 22%  5% 35%
[libx264 @ 0x2d8dd80] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 25% 23% 25%  4%  6%  5%  6%  4%  4%
[libx264 @ 0x2d8dd80] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 20% 33%  5%  6%  5%  5%  4%  3%
[libx264 @ 0x2d8dd80] i8c dc,h,v,p: 63% 20% 13%  4%
[libx264 @ 0x2d8dd80] Weighted P-Frames: Y:28.4% UV:27.0%
[libx264 @ 0x2d8dd80] ref P L0: 67.9% 12.2% 14.6%  4.9%  0.4%
[libx264 @ 0x2d8dd80] ref B L0: 94.3%  4.8%  0.9%
[libx264 @ 0x2d8dd80] ref B L1: 98.2%  1.8%
[libx264 @ 0x2d8dd80] kb/s:1253.22
[libx264 @ 0x2de9c00] frame I:3     Avg QP:18.17  size: 15799
[libx264 @ 0x2de9c00] frame P:132   Avg QP:22.99  size:  5465
[libx264 @ 0x2de9c00] frame B:266   Avg QP:26.61  size:  1050
[libx264 @ 0x2de9c00] consecutive B-frames: 10.0%  3.0%  5.2% 81.8%
[libx264 @ 0x2de9c00] mb I  I16..4: 45.1% 43.3% 11.7%
[libx264 @ 0x2de9c00] mb P  I16..4:  6.1%  8.5%  0.5%  P16..4: 42.7% 12.0%  6.5%  0.0%  0.0%    skip:23.8%
[libx264 @ 0x2de9c00] mb B  I16..4:  0.1%  0.1%  0.0%  B16..8: 30.1%  3.0%  0.6%  direct: 2.1%  skip:64.0%  L0:38.0% L1:55.4% BI: 6.6%
[libx264 @ 0x2de9c00] 8x8 transform intra:54.3% inter:64.3%
[libx264 @ 0x2de9c00] coded y,uvDC,uvAC intra: 30.7% 42.3% 6.9% inter: 7.3% 10.8% 0.5%
[libx264 @ 0x2de9c00] i16 v,h,dc,p: 36% 22%  6% 36%
[libx264 @ 0x2de9c00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 22% 21% 24%  4%  6%  6%  7%  4%  5%
[libx264 @ 0x2de9c00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 22% 21% 23%  6%  8%  6%  6%  5%  4%
[libx264 @ 0x2de9c00] i8c dc,h,v,p: 63% 20% 13%  5%
[libx264 @ 0x2de9c00] Weighted P-Frames: Y:25.0% UV:22.7%
[libx264 @ 0x2de9c00] ref P L0: 65.8% 15.4% 13.4%  5.0%  0.4%
[libx264 @ 0x2de9c00] ref B L0: 95.2%  4.1%  0.7%
[libx264 @ 0x2de9c00] ref B L1: 98.3%  1.7%
[libx264 @ 0x2de9c00] kb/s:626.67
[libx264 @ 0x2dee860] frame I:3     Avg QP:18.31  size: 11356
[libx264 @ 0x2dee860] frame P:130   Avg QP:23.11  size:  3716
[libx264 @ 0x2dee860] frame B:268   Avg QP:26.88  size:   592
[libx264 @ 0x2dee860] consecutive B-frames:  9.2%  3.5%  4.5% 82.8%
[libx264 @ 0x2dee860] mb I  I16..4: 42.9% 43.6% 13.5%
[libx264 @ 0x2dee860] mb P  I16..4:  4.5%  8.6%  0.7%  P16..4: 42.2% 15.0%  7.7%  0.0%  0.0%    skip:21.3%
[libx264 @ 0x2dee860] mb B  I16..4:  0.2%  0.2%  0.0%  B16..8: 30.3%  2.7%  0.6%  direct: 2.0%  skip:64.0%  L0:36.6% L1:57.5% BI: 5.9%
[libx264 @ 0x2dee860] 8x8 transform intra:58.8% inter:59.5%
[libx264 @ 0x2dee860] coded y,uvDC,uvAC intra: 35.8% 47.0% 8.6% inter: 7.8% 10.4% 0.8%
[libx264 @ 0x2dee860] i16 v,h,dc,p: 35% 25%  7% 33%
[libx264 @ 0x2dee860] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 23% 24% 21%  4%  6%  5%  6%  4%  6%
[libx264 @ 0x2dee860] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 30% 18%  5%  7%  6%  6%  4%  4%
[libx264 @ 0x2dee860] i8c dc,h,v,p: 59% 22% 13%  5%
[libx264 @ 0x2dee860] Weighted P-Frames: Y:21.5% UV:18.5%
[libx264 @ 0x2dee860] ref P L0: 64.5% 17.5% 12.8%  5.0%  0.2%
[libx264 @ 0x2dee860] ref B L0: 94.1%  4.9%  1.0%
[libx264 @ 0x2dee860] ref B L1: 98.0%  2.0%
[libx264 @ 0x2dee860] kb/s:404.07
[libx264 @ 0x2df1400] frame I:2     Avg QP:18.75  size:  7873
[libx264 @ 0x2df1400] frame P:143   Avg QP:23.38  size:  1808
[libx264 @ 0x2df1400] frame B:256   Avg QP:27.86  size:   178
[libx264 @ 0x2df1400] consecutive B-frames: 13.5%  3.0%  3.7% 79.8%
[libx264 @ 0x2df1400] mb I  I16..4: 56.9% 23.1% 20.0%
[libx264 @ 0x2df1400] mb P  I16..4:  3.2%  6.0%  0.4%  P16..4: 41.8% 18.2%  9.7%  0.0%  0.0%    skip:20.8%
[libx264 @ 0x2df1400] mb B  I16..4:  0.1%  0.0%  0.0%  B16..8: 30.1%  1.3%  0.3%  direct: 1.0%  skip:67.1%  L0:33.7% L1:63.0% BI: 3.4%
[libx264 @ 0x2df1400] 8x8 transform intra:57.2% inter:54.7%
[libx264 @ 0x2df1400] coded y,uvDC,uvAC intra: 40.7% 48.7% 11.3% inter: 8.7% 10.8% 1.4%
[libx264 @ 0x2df1400] i16 v,h,dc,p: 44% 20%  8% 28%
[libx264 @ 0x2df1400] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 26% 20%  5%  7%  6%  8%  5%  7%
[libx264 @ 0x2df1400] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 25% 14%  6%  9%  7%  8%  7%  6%
[libx264 @ 0x2df1400] i8c dc,h,v,p: 61% 22% 12%  5%
[libx264 @ 0x2df1400] Weighted P-Frames: Y:19.6% UV:17.5%
[libx264 @ 0x2df1400] ref P L0: 63.5% 21.5% 10.5%  4.4%  0.0%
[libx264 @ 0x2df1400] ref B L0: 95.3%  3.8%  0.8%
[libx264 @ 0x2df1400] ref B L1: 98.0%  2.0%
[libx264 @ 0x2df1400] kb/s:191.33
[libx264 @ 0x2dcf1e0] frame I:3     Avg QP:20.44  size:  3117
[libx264 @ 0x2dcf1e0] frame P:258   Avg QP:23.63  size:   482
[libx264 @ 0x2dcf1e0] frame B:140   Avg QP:28.53  size:    58
[libx264 @ 0x2dcf1e0] consecutive B-frames: 52.1%  3.0%  3.0% 41.9%
[libx264 @ 0x2dcf1e0] mb I  I16..4: 37.5% 47.2% 15.3%
[libx264 @ 0x2dcf1e0] mb P  I16..4:  1.3%  2.8%  0.5%  P16..4: 34.8% 13.6%  7.5%  0.0%  0.0%    skip:39.4%
[libx264 @ 0x2dcf1e0] mb B  I16..4:  0.1%  0.1%  0.0%  B16..8: 23.6%  0.5%  0.1%  direct: 0.3%  skip:75.4%  L0:24.2% L1:73.3% BI: 2.5%
[libx264 @ 0x2dcf1e0] 8x8 transform intra:57.7% inter:58.0%
[libx264 @ 0x2dcf1e0] coded y,uvDC,uvAC intra: 46.2% 56.9% 18.9% inter: 11.2% 13.8% 2.6%
[libx264 @ 0x2dcf1e0] i16 v,h,dc,p: 51% 18% 11% 21%
[libx264 @ 0x2dcf1e0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 28% 21%  5%  7%  5%  9%  5%  9%
[libx264 @ 0x2dcf1e0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu:  8% 53%  9%  4%  6%  5%  6%  3%  7%
[libx264 @ 0x2dcf1e0] i8c dc,h,v,p: 57% 27% 10%  5%
[libx264 @ 0x2dcf1e0] Weighted P-Frames: Y:10.5% UV:8.9%
[libx264 @ 0x2dcf1e0] ref P L0: 68.0% 21.4%  7.2%  3.4%  0.0%
[libx264 @ 0x2dcf1e0] ref B L0: 90.9%  6.8%  2.3%
[libx264 @ 0x2dcf1e0] ref B L1: 97.6%  2.4%
[libx264 @ 0x2dcf1e0] kb/s:84.71

real    0m35.185s
user    4m51.602s
sys 0m30.390s

A fusão não vai me ajudar aqui, porque o segundo vídeo é enviado pelo cliente e pode estar em muitos formatos e codecs diferentes (avi, mp4, mpeg, mpg, ts, mp4 ...) meu pensamento original era converter os dois vídeos para mp4 e se juntar a eles, mas que eu tenho problema com dois átomos MOOV e não é adequado para streaming Como mesclar 2 arquivos mp4 com 1 átomo?

Você precisa concatenar a introdução e o arquivo principal. A menos que eu tenha entendido mal sua exigência. Você pode usar o desmuxer; filtro; ou métodos de protocolo. Veja isso:

http://ffmpeg.org/trac/ffmpeg/wiki/How%20to%20concatenate%20%28join,%20merge%29%20media%20files

e isto:

http://ffmpeg.org/ffmpeg-filters.html#concat

Você diz que o segundo vídeo pode estar em uma variedade de formatos. Nesse caso, a recodificação é a única opção. O filtro parece funcionar nesses cenários.