Just a note for other people that read this. I had the same problem
described here on Ubuntu 10.10 beta, and also thought it must be some
CPU scaling problem, but like Oliver it turned out to be a GPU scaling
issue (running glxgears made it go away).

I have found the easiest way to fix this is to change the Preferred Mode
under PowerMizer in the NVIDIA X Server Settings to "Prefer Maximum
Performance" rather than "Adaptive". I'm not sure if there is anything
less rigorous, but that fixed it for me.

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CPU Scaling too aggressive
https://bugs.launchpad.net/bugs/107545
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