uname -a
Linux hades 3.13.0-34-generic #60-Ubuntu SMP Wed Aug 13 15:45:27 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux


Command for recording:
ffmpeg -r 30 -f x11grab -s 1280:720 -i :0.0+0,58 -map 0 -vcodec libx264 -preset ultrafast "${BASE_DIR}${1}/${1}.mkv" -f alsa -i pulse -map 1 -ac 2 -ar 44100 -acodec libvorbis "${BASE_DIR}${1}/${1}_track1.ogg" -f alsa -ar 44100 -i pulse -map 2 -acodec libvorbis -ac 2 "${BASE_DIR}${1}/${1}_track2.ogg"


Result file info:
ffmpeg -i test.mkv -i test_track2.ogg
ffmpeg version 1.2.6-7:1.2.6-1~trusty1 Copyright (c) 2000-2014 the FFmpeg developers
  built on Apr 26 2014 18:52:58 with gcc 4.8 (Ubuntu 4.8.2-19ubuntu1)
  configuration: --arch=amd64 --disable-stripping --enable-avresample --enable-pthreads --enable-runtime-cpudetect --extra-version='7:1.2.6-1~trusty1' --libdir=/usr/lib/x86_64-linux-gnu --prefix=/usr --enable-bzlib --enable-libdc1394 --enable-libfreetype --enable-frei0r --enable-gnutls --enable-libgsm --enable-libmp3lame --enable-librtmp --enable-libopencv --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-vaapi --enable-vdpau --enable-libvorbis --enable-libvpx --enable-zlib --enable-gpl --enable-postproc --enable-libcdio --enable-x11grab --enable-libx264 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  avcodec     configuration: --arch=amd64 --disable-stripping --enable-avresample --enable-pthreads --enable-runtime-cpudetect --extra-version='7:1.2.6-1~trusty1' --libdir=/usr/lib/x86_64-linux-gnu --prefix=/usr --enable-bzlib --enable-libdc1394 --enable-libfreetype --enable-frei0r --enable-gnutls --enable-libgsm --enable-libmp3lame --enable-librtmp --enable-libopencv --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-vaapi --enable-vdpau --enable-libvorbis --enable-libvpx --enable-zlib --enable-gpl --enable-postproc --enable-libcdio --enable-x11grab --enable-libx264 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static --enable-version3 --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libvo-aacenc --enable-libvo-amrwbenc
  libavutil      52. 18.100 / 52. 18.100
  libavcodec     54. 92.100 / 54. 92.100
  libavformat    54. 63.104 / 54. 63.104
  libavdevice    53.  5.103 / 53.  5.103
  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, matroska,webm, from 'test.mkv':
  Metadata:
    ENCODER         : Lavf54.63.104
  Duration: 00:02:17.93, start: 0.000000, bitrate: 8507 kb/s
    Stream #0:0: Video: h264 (High 4:4:4 Predictive), yuv444p, 1280x720, SAR 1:1 DAR 16:9, 30 fps, 30 tbr, 1k tbn, 60 tbc (default)
Input #1, ogg, from 'test_track2.ogg':
  Duration: 00:02:18.36, start: 0.000000, bitrate: 102 kb/s
    Stream #1:0: Audio: vorbis, 44100 Hz, stereo, fltp, 112 kb/s
    Metadata:
      ENCODER         : Lavf54.63.104
At least one output file must be specified
geiger@hades:~/youtube/test$ uname -a
Linux hades 3.13.0-34-generic #60-Ubuntu SMP Wed Aug 13 15:45:27 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
geiger@hades:~/youtube/test$ ffmpeg -i test.mkv -i test_track2.ogg
ffmpeg version 1.2.6-7:1.2.6-1~trusty1 Copyright (c) 2000-2014 the FFmpeg developers
  built on Apr 26 2014 18:52:58 with gcc 4.8 (Ubuntu 4.8.2-19ubuntu1)
  configuration: --arch=amd64 --disable-stripping --enable-avresample --enable-pthreads --enable-runtime-cpudetect --extra-version='7:1.2.6-1~trusty1' --libdir=/usr/lib/x86_64-linux-gnu --prefix=/usr --enable-bzlib --enable-libdc1394 --enable-libfreetype --enable-frei0r --enable-gnutls --enable-libgsm --enable-libmp3lame --enable-librtmp --enable-libopencv --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-vaapi --enable-vdpau --enable-libvorbis --enable-libvpx --enable-zlib --enable-gpl --enable-postproc --enable-libcdio --enable-x11grab --enable-libx264 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  avcodec     configuration: --arch=amd64 --disable-stripping --enable-avresample --enable-pthreads --enable-runtime-cpudetect --extra-version='7:1.2.6-1~trusty1' --libdir=/usr/lib/x86_64-linux-gnu --prefix=/usr --enable-bzlib --enable-libdc1394 --enable-libfreetype --enable-frei0r --enable-gnutls --enable-libgsm --enable-libmp3lame --enable-librtmp --enable-libopencv --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-vaapi --enable-vdpau --enable-libvorbis --enable-libvpx --enable-zlib --enable-gpl --enable-postproc --enable-libcdio --enable-x11grab --enable-libx264 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static --enable-version3 --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libvo-aacenc --enable-libvo-amrwbenc
  libavutil      52. 18.100 / 52. 18.100
  libavcodec     54. 92.100 / 54. 92.100
  libavformat    54. 63.104 / 54. 63.104
  libavdevice    53.  5.103 / 53.  5.103
  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, matroska,webm, from 'test.mkv':
  Metadata:
    ENCODER         : Lavf54.63.104
  Duration: 00:02:17.93, start: 0.000000, bitrate: 8507 kb/s
    Stream #0:0: Video: h264 (High 4:4:4 Predictive), yuv444p, 1280x720, SAR 1:1 DAR 16:9, 30 fps, 30 tbr, 1k tbn, 60 tbc (default)
Input #1, ogg, from 'test_track2.ogg':
  Duration: 00:02:18.36, start: 0.000000, bitrate: 102 kb/s
    Stream #1:0: Audio: vorbis, 44100 Hz, stereo, fltp, 112 kb/s
    Metadata:
      ENCODER         : Lavf54.63.104
At least one output file must be specified