FFmpeg sets incorrect codec in output stream with multiple maps

[mt]

Summary of the bug:
When transcoding FFmpeg incorrectly sets the audio codec with multiple maps. It simply takes the last one and applies it to all audio tracks.

All FFmpeg version from 0.9 are affected by this.

How to reproduce:

ffmpeg -i input.mkv -map 0:0 -vcodec copy -map 0:1 -acodec aac -map 0:2 -acodec alac test.m4v
ffmpeg version 1.2 Copyright (c) 2000-2013 the FFmpeg developers
  built on Apr  2 2013 22:14:15 with llvm-gcc 4.2.1 (LLVM build 2336.11.00)
  configuration: 
  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
Input #0, matroska,webm, from 'input.mkv':
  Duration: 00:51:41.38, start: 0.000000, bitrate: 8640 kb/s
    Stream #0:0: Video: h264 (High), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
    Stream #0:1(ger): Audio: dts (DTS), 48000 Hz, 5.1(side), fltp, 768 kb/s (default) (forced)
    Stream #0:2(eng): Audio: dts (DTS), 48000 Hz, 5.1(side), fltp, 1536 kb/s
[alac @ 0x7ffa6391b600] encoding as 24 bits-per-sample
[alac @ 0x7ffa6391bc00] encoding as 24 bits-per-sample
Output #0, ipod, to 'test.m4v':
  Metadata:
    encoder         : Lavf54.63.104
    Stream #0:0: Video: h264 (avc1 / 0x31637661), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], q=2-31, 23.98 fps, 16k tbn, 1k tbc (default)
    Stream #0:1(ger): Audio: alac (alac / 0x63616C61), 48000 Hz, 5.1, s32p, 128 kb/s (default) (forced)
    Stream #0:2(eng): Audio: alac (alac / 0x63616C61), 48000 Hz, 5.1, s32p, 128 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #0:1 -> #0:1 (dca -> alac)
  Stream #0:2 -> #0:2 (dca -> alac)

[Carl Eugen Hoyos]

Not audio specific:
$ ffmpeg -i fate-suite/svq3/Vertical400kbit.sorenson3.mov -vcodec mpeg1video -map 0:0 -acodec ac3 -map 0:1 -vcodec flv -map 0:0 -acodec mp2 -map 0:1 -y out.avi

[Carl Eugen Hoyos]

(I suspect other users would have answered faster if you had asked on ffmpeg-users.)

You need to specify the audio stream number, this is explained on ​http://ffmpeg.org/ffmpeg.html#Main-options
For my command line, this would be:
$ ffmpeg -i fate-suite/svq3/Vertical400kbit.sorenson3.mov -codec:v:0 mpeg1video -map 0:0 -codec:a:0 ac3 -map 0:1 -codec:v:1 flv -map 0:0 -codec:a:1 mp2 -map 0:1 -y out.avi

In your case, it is something like:
$ ffmpeg -i input.mkv -map 0:0 -vcodec copy -map 0:1 -codec:a:0 aac -map 0:2 -codec:a:1 alac test.m4v

Sorry for not realizing this earlier!