Thanks lca77,
I don't think that is the problem, since version 0.3 doesn't have any problems with MP2 (it has others, for it is an older version), though it is based on the same mencoder version. It is a certain bug. Nevertheless I'll try older mencoder version.
Once more:
1. the resulting video files are "not prepared for sequential reading" if the output audio track is MP2.
2. The source resolution is read wrong for some VOB or MKV files. It seems that the program replaces the source frame width with 720, if the frames are wider than it. As a result the aspect ratio is invalid.
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