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0e1f616
(Get the code!)
To me it looks like video and audio keeps having sync issues with any player when pulseaudio is involved (totem, mplayer, mythtv, flashplugin, vlc, ffplay).
The results are better for players that use gstreamer with pulse disabled (kill daemon and disable autospawn). Ditto for mplayer with direct ALSA output. Sending sound through jackd also works fine for players that support it.
It looks like this is a problem which has been introduced somewhere between pulseaudio 0.9.10 (intrepid) and 0.9.14 (jaunty). At some point I tried 0.9.14 with intrepid, but reverted to 0.9.10 because of this problem. I've tried pulseaudio 0.9.15 with both intrepid and jaunty, and that makes the problem even worse. A kernel with CONFIG_HZ_1000=y as recommended by pulse developers show some improvement, but doesn't completely solve the problem.
Debugging with mythtv (svn trunk) indicate that audio latency varies a lot (40-200ms) when pulseaudio 0.9.14/15 is used, but remains fairly constant (~40ms) with pulseaudio 0.9.10. Could this be the cause? These numbers are from a E6600 system with an ASUS Xonar DX soundcard (snd_virtuoso). Numbers differ slightly with other soundcards, but the symptoms are the same.