I had a problem like this on a amd build. I swapped cards and all that and nothing fixed it. odd thing was it only started after I downloaded the latest drivers for them but thinking it was the drivers I used older versions and it didn't do anything to fix it. Would run games perfect but would have random lag spikes and games like x3, teh menus would lag like nothing else. I just ended up getting a nvidia card. Not saying that's the fix , it's just what I did.