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".