Writing application : mkvmerge v4.2.0 ('No Talking') built on Jul 29 2010 11:34:44
Why does audio or video not play anymore since v4.1.0 (e.g. MP3, AC3, DTS audio tracks, h264 video tracks)?
The Matroska specifications know a feature called "header removal compression". This allows a muxer to keep a certain number of bytes that are identical for each frame in the track headers removing them from the individual frames. This reduces the size of the tracks significantly without altering the content as a demuxer can add the bytes found in the track headers to each frame during demuxing.
Starting with v4.1.0 mkvmerge uses header removal compression for a couple of track types by default. These include AC3, DTS and MP3 audio tracks as well as Dirac and MPEG-4 part 2 (aka. XviD/DivX) video tracks. The user muxing a file may disable it by explicitely selecting 'none' as the compression scheme for such a track.
If your player has difficulties playing such files then it is a bug in that player or in the demuxer but not in mkvmerge. This feature has been part of the Matroska specification since more than six years, and there's no excuse for refusing to add support for it.
The proper solution is to ask the vendor of your player to support this feature. A temporary solution is to re-mux such files turning off extra compression for all tracks.