Actually, thermal compound conducts heat rather well. That ensures quick heat transfer from chip to heatsink.
Something to consider: your fan. Is it plugged in? If it is, did your bios change the fan speed? Some bioses are set to run the fan at a decreased speed.
If it's because of overheating, clean the dust out of your box, then run a game for 5 minutes, reboot, and check the temperatures in your dashboard. WRITE THEM DOWN. Then run a game for 10 more minutes, check, then another 10 and check. WRITE DOWN THE TEMPS.
Then, post them here. Or check the Pinned/FAQs section to see what ideal and normal temps are for components. You might find it IS a heat issue, or it may be something deeper.