I joined the mplayer mailing list and have tried to seek help/information from those nice folks..  The following is part of one of my exchanges.  Maybe the part about the timestamp may be of some help?

> I asked a couple specific questions and included some quotes from other
> posts to provide an idea of what we're looking at as the cause.  I can't
> tell you what the exact problem is because we're still trying to figure that
> out...  And a good place to start is by comparing the differences between
> the software that has the problem and software that doesn't.  We're
> trying to figure out what mplayer does, if anything, with regards to
> repacking, the pes layer, pcr data, etc. during the "playback" of a VDR "recording".

nothing particular: the pes packetization is as standard as you can get,
except that IIRC there's a timestamp on every single frame,
rather than once every 0.5-0.7 seconds; this fact alone can make a
lot of difference during playback.
Does the desync that you are experiencing get worse with time or does
it regularly decrease and next increase?

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