I had same setup and running Gentoo.
I had the same exact problem you did infernator your methods worked for fixing my problem.. I also to had the same thing happen with glxgears, in the background i get 10,000fps in foreground I get 5,000fps..
The big key for me was taking out the dri rendering from the kernel,, i had already taken out the agpart,, and i had tried NvAGP 1,2, and3 but not4 in the options of Xf86Config..
Thanks again for posting info