Actually, on my machine DISABLING sync to vBlank(in both Nvidia settings
and ccsm),  not enabling it (which is enabled by default)  partially
works around the problem (it does not work for full screen), see my post
#3

If furthermore, "undericted fullscreen windows" is checked in ccsm then
vdpau works perfectly in XBMC but still not work for mplayer and
mplayer2. But it has other side effects such as tearing for Desktop
cube.

IIRC there is an option in KDE which disables Desktop compositing for
fullscreen applications, I think something like that would probably
solve the problem if available in Unity.

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https://bugs.launchpad.net/bugs/993397

Title:
  vdpau not working (well) with Ubuntu12.04 Unity

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