AC3 audio doesn't work properly inside MP4 container.
As reported in: http://forum.videolan.org/viewtopic.php?p=184974#p184974
AC3 audio inside MP4 container doesn't work properly in VLC. There are two issues:
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You cannot select SPDIF output for AC3 audio if it is inside MP4 container.
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Channel mappings are wrong when AC3 is inside MP4.
Sample file available in: http://public.me.com/dan_isaacs and another sample in http://www.dvbportal.com/ts/Heroes.S3E2.6CH.HD-sample.m4v (on both videos AAC audio track is the first one and AC3 is the second one)
and some interesting discussion http://forum.doom9.org/showthread.php?p=1211486#post1211486
Tested on 0.9.8a and vlc-git 1.0.0 20090211 under Win32.