I did try the free version of 3dmark, and man did it bring my system to a crawl (couldn't change settings to reflect what I tend to run games at). The only thing getting hot is the video card, topping out at 69° C, but even when it's running cool, I still have the problems. (If it was just a hot card, wouldn't the problem stay once it got too hot? Like I've mentioned, this is an almost cyclical problem, ebbing and flowing in a regular pattern)
Thanks for the suggestions. I'll try them.
Well I don't think it's just a hot video card, as you wouldn't have had the problem with the other vid card. It would make sense if it was hot chipset or CPU though, as it would get hot, throttle itself to cool down, and then heat back up. So it would be cyclical like what you describe.
Have you had a chance to try the large household fan? That would rule out heat(as it would be blowing on the chipset as well, and would be giving you lots of cool air on it).
Do you have a different power supply you could try? I would also try clearing your bios back to factory settings in case some weird setting got changed.
If none of that works, I'd probably just buy a new motherboard. Time is money, and the more time you spend on this, the less money spending another $50-$60 on a motherboard seems. According to a newegg review of your motherboard:
"where to start, the board didnt work right out of the box had to clear the cmos, then it would boot because of having two sticks of memory. after I messed with it for awhile it ran windows ok but games was a whole other thing. I have a athlon x2 6000+, 9600gt 2 gigs ram, 250 gig sata hd and had fps randging from 5 to 95 on call of duty 5 tried everythin nothing helped bought a new msi k9a2 neo-f and my fps went to 60 to over a hundred on high setting with all the same stuff except the motherboard."
Seems there was a decent amount of people having trouble with that motherboard. Might be worth trying to RMA it as well.