I think you can just disable GLXVBlank in xorg.conf (Option "GLXVBlank" "False"), which is probably in the Device section.
<device screen="0" driver="dri2">
<option name="vblank_mode" value="0" />
Consider vblank_mode option 0 or 1 disable vblank, 2 or 3 enable it; you need to reboot after the configuration of .drirc file.
Any chance for this ppa to host the latest released intel-vaapi driver 1.19, it has many improvements over the one thats included in Ubuntu 12.10, that one is version 1.17
If you care you may ask the Debian maintainer to update to 1.19.
I gave it a try again. Unsuccess: with Radeon driver on HD5770 I got mixed results. While some loads are really faster, better and so on, in Xonotic it got horribly broken. While usual FPS is about matching with screen FPS, it can drop as bad as 2FPS on some scenes. Which makes xonotic really unplayable.
So I had to revert this driver to stock. Probably it haves something to do with these tests and these patches. Looks like I got hit by the very same problem during test run.
xswat ppa has the latest intel-vaapi driver version 1.19, would truly appreciate if this can be ported to the ppa as I would really not like to add another ppa related to video stack.