Ага, такая же ошибка :( Но если немного по-другому задать параметры кодирования, то всё будет норм:

Смотрим доступные дорожки в файле:

$  ffmpeg -i Darker_than_Black\ _01.mkv
FFmpeg version SVN-r20822, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  built on Dec 13 2009 16:06:17 with gcc 4.4.2
  configuration: --prefix=/usr --enable-gpl --enable-nonfree --enable-libmp3lame --enable-libvorbis --enable-shared --enable-pthreads --enable-x11grab --enable-postproc --enable-libfaac --enable-libfaad --enable-libxvid --enable-libtheora --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libx264 --enable-version3 --disable-stripping
  libavutil     50. 6. 0 / 50. 6. 0
  libavcodec    52.43. 0 / 52.43. 0
  libavformat   52.41. 0 / 52.41. 0
  libavdevice   52. 2. 0 / 52. 2. 0
  libswscale     0. 7. 1 /  0. 7. 1
  libpostproc   51. 2. 0 / 51. 2. 0
[matroska @ 0x8249380]max_analyze_duration reached
[matroska @ 0x8249380]Estimating duration from bitrate, this may be inaccurate
Seems stream 0 codec frame rate differs from container frame rate: 47.95 (48000/1001) -> 23.98 (24000/1001)
Input #0, matroska, from 'Darker_than_Black _01.mkv':
  Duration: 00:24:20.05, start: 0.000000, bitrate: N/A
    Stream #0.0(jpn): Video: h264, yuv420p, 1280x720, PAR 1:1 DAR 16:9, 23.98 tbr, 1k tbn, 47.95 tbc
    Stream #0.1(rus): Audio: aac, 44100 Hz, stereo, s16
    Stream #0.2(jpn): Audio: aac, 48000 Hz, stereo, s16
    Stream #0.3(rus): Subtitle: 0x0000
  Metadata
    title           : The Star of Contract Flowed... (First Volume)
At least one output file must be specified

Извлекаем русскую дорожку с пережатием в mp3:

ffmpeg -i Darker_than_Black\ _01.mkv -map 0:1 -vn -ar 44100 -ac 2 -ab 128 -f mp3 audio.mp3