I've got the same basic problem here, but not quite as severe. I can usually get all the way through Freespace, but on the rare occasion it'll lock up. Another one that locks up a lot is the Subspace plugin for AmigaAmp. Usually I can run any SINGLE ppc task for any length of time. It's when I run multiple ppc tasks that it craps out.
The only thing I wonder about overheating is, why, when I reboot and go right back to the program that caused it to overheat, does it then run okay for an hour or so before the next crash. If it's overheating, wouldn't it take longer than the time it takes to reboot (about 7 seconds) to cool down?