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I have playback problems with native Mpeg 4 ASP in mkv.
Take a look at the picture:


I created an AVI(XviD) with avidemux 2.1 ( http://www.avidemux.org/ ) and muxed it with mkvmerge --engage native_mpeg4 (mkvtoolnix 1.6.5).

For playback I used VLC SVN from today morning.

I have uploaded a sample ( native-mpeg4.mkv ) to streams.videolan.org/incoming.

--engage native_mpeg4 in mkvtoolnix is known to have problems. Don't use it for the moment.