Happens a fair bit with Thermaltake Coolers, its their terrible mounting system combined with a shift of weight from the bottom to bottom/fairly even to a very topheavy cooler.

Mounted in a tower case if any of the nuts holding the cooler on loosen a bit you will start to make less contact with the CPU and eventually the thing will turn itself to prevent overheating.

This has happened to me with both a Tt SilentTower and a BigTyphoon.

I installed a large copper heatsink in my rig, a thing of beauty it was too.
My PC would crash every so often, swapped out just about everything.
Then I place the motherboard horizontally - no more problem!
I think the weight (and height) of the cooler was distorting the mobo, replaced it with the cheaper alumunium/copper version and the problem was gone for good.
eBay'd the all-copper one.

What no stats with the cpu running at full load? Also with the cpu at idle the fan should be silent, duh.