I can't say that I am any better . I have a PCI-e card myself: 8800gts OC, which is why I was confused that it was enabled.
I am not near my desktop right now, but if you run dxdiag, I believe the setting was on the display tab. There were three settings: direct draw, direct 3d, and agp texture acceleration. I left the first two enabled, and disabled the last one. I then rebooted (don't know if it was necessary, but it couldn't hurt.)
Thanks
A