https://bugs.freedesktop.org/show_bug.cgi?id=66384
--- Comment #6 from nfxjfg@gmail.com --- Shouldn't this be responsibility of the code that implements the vdpau API? Maybe it should attempt to remap the MSC counters to system time, and smooth out the differences. (Sorry I don't know anything about Mesa internals.)
IMO this issue does make the Mesa vdpau implementation very unreliable, and at least for me it has caused a lot of problems.