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Ah... output files mkvB & mkvC are different just enough, so that they behave differently when played.
I've encountered something similar. I can have three non-identical copies of a video track (demuxed from .TS, or demuxed from .M2TS using eac3to, or extracted from .M2TS into .MKV using eac3to) and mkvmerge will accept all three tracks. But the output .MKV files don't play back identically in mpc-hc.
In my mind, Audio+Video->MKV should work no matter where I get the source files, but that isn't always the case. I don't have any samples handy now, however.
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