I applied the thermal compound using the Quad Core aproved method on Artic Silver's website.
Doesn't matter. A little too much or a little too little and you can have a problem. Or you might have rocked the HS/Fan putting it on and created a small air pocket.
Regardlass, if the CPU temps aren't going too high under a stress test then that's not the problem. My guess is the CPU is running out of voltage.