How did you check the CPU temperature? The BIOS can sometimes get it wrong if it's not properly set up for your CPU. Try CoreTemp or RealTemp; if they give the same readings then you have a problem. I would say that anything over about 60 under load, or 40 when idling, is getting too high. I would expect lower temperatures than these in practice.
Overheating would certailnly explain your symptoms, particularly as they happen at the "expanding files" stage, when you would expect the CPU to be working a little harder.