Please see bug 807 at https://roundup.ffmpeg.org/roundup/ffmpeg/issue807


There are two files here which show the problem - non_monotone_timestamps[01].mkv 


The output of the latest build of FFMPEG on the first file is:

andy@pain$ ffmpeg -y -i non_monotone_timestamps0.mkv -acodec ac3 -ab 640k -vcodec copy /tmp/test.mkv
FFmpeg version SVN-r16845, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  configuration: --prefix=/usr/local --disable-debug --enable-shared --enable-gpl --enable-postproc --enable-swscale --enable-pthreads --enable-x11grab --enable-libdc1394 --enable-libfaac --enable-libfaad --enable-libgsm --enable-libmp3lame --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid
  libavutil     49.14. 0 / 49.14. 0
  libavcodec    52.11. 0 / 52.11. 0
  libavformat   52.25. 0 / 52.25. 0
  libavdevice   52. 1. 0 / 52. 1. 0
  libswscale     0. 6. 1 /  0. 6. 1
  libpostproc   51. 2. 0 / 51. 2. 0
  built on Jan 28 2009 14:41:55, gcc: 4.3.2
Input #0, matroska, from 'sample.mkv':
  Duration: 02:01:33.82, start: 0.000000, bitrate: N/A
    Stream #0.0: Video: h264, yuv420p, 960x544, PAR 213:160 DAR 639:272, 23.98 tb(r)
    Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, s16
Output #0, matroska, to '/tmp/test.mkv':
    Stream #0.0: Video: libx264, yuv420p, 960x544 [PAR 213:160 DAR 639:272], q=2-31, 1000.00 tb(c)
    Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, s16, 640 kb/s
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Press [q] to stop encoding
[NULL @ 0x13b0420]error, non monotone timestamps 709 >= 42
av_interleaved_write_frame(): Error while opening file

And the output of the second is

andy@pain$ ffmpeg -i non_monotone_timestamps1.mkv -acodec ac3 -ab 640k -vcodec copy test.mkv
FFmpeg version SVN-r16845, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  configuration: --prefix=/usr/local --disable-debug --enable-shared --enable-gpl --enable-postproc --enable-swscale --enable-pthreads --enable-x11grab --enable-libdc1394 --enable-libfaac --enable-libfaad --enable-libgsm --enable-libmp3lame --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid
  libavutil     49.14. 0 / 49.14. 0
  libavcodec    52.11. 0 / 52.11. 0
  libavformat   52.25. 0 / 52.25. 0
  libavdevice   52. 1. 0 / 52. 1. 0
  libswscale     0. 6. 1 /  0. 6. 1
  libpostproc   51. 2. 0 / 51. 2. 0
  built on Jan 28 2009 14:41:55, gcc: 4.3.2
Input #0, matroska, from 'non_monotone_timestamps1.mkv':
  Duration: 01:57:46.67, start: 0.000000, bitrate: N/A
    Stream #0.0(eng): Video: h264, yuv420p, 1280x688, PAR 1:1 DAR 80:43, 23.98 tb(r)
    Stream #0.1: Audio: dca, 48000 Hz, 5.1, s16
Output #0, matroska, to 'test.mkv':
    Stream #0.0(eng): Video: libx264, yuv420p, 1280x688 [PAR 1:1 DAR 80:43], q=2-31, 1000.00 tb(c)
    Stream #0.1: Audio: ac3, 48000 Hz, 5.1, s16, 640 kb/s
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Press [q] to stop encoding
[NULL @ 0x187c350]error, non monotone timestamps 167 >= 83
av_interleaved_write_frame(): Error while opening file: