I know what you are talking about, I get it too sometimes, but at high settings 1280x1024 with 2x AA, it only happens when I have the AA on
Bump up the grpahics 1024x768 or 1280x1024 because running at 800x600 is putting more stress on the CPU than the graphics card
I ran BF2 at low settings and it sucked and I had terrible framerate, moved it up to normal high settings and the highest res and I was getting the normal 80+ FPS.