Well, here's the result: it still happens, although it's a lot less noticable than it used to be.
I'm now runnig the latest Ubuntu beta, the graphics card is a nvidia 8800gtx. The driver version is 185.18.36.
Everytime it happens, the cpu usage goes down in the process viewer.
The application now shows up with 64% cpu (I think they changed to relative cpu usage to core usage) usage which drops to ~40% every time it happens (used to show around 15% with drops to 1-2%, this probably explains why its less noticable now). The opengl sample now uses 44% and drops to 30% cpu.
But lets wait if someone else notices the same (and who knows, the problem may disappear before a final 2.0 release
.