I recently assembled a new PC with a Core 2 Duo E6600 processor and MSI P965 Neo-F motherboard. The CPU fan is Intel's default one, and I'm pretty sure it's properly attached (haven't yet double-checked, but the fan did click into place). I'm getting an idle CPU temp of about 50 C and under load 78-80 C (yikes!). These numbers I get from /proc/cpuinfo in Linux.

The fun doesn't stop there. First of all, when I boot into BIOS setup the System Health menu claims the temp is about 90 C. That's strange because the CPU should be idle. Maybe the BIOS is buggy and it's really Fahrenheit (90 C is 32 F), I don't know -- but that wouldn't explain why in Linux the idle temp is 50 C.

All this is probably nothing that a good CPU fan won't fix, but I'm getting weird power offs too. And they only happen in the GRUB boot menu! In BIOS setup or in Linux nothing like that happens, I just see alarming temps. But in the boot menu it may just power off without any warning at any moment, usually within 10 seconds. It happens in Knoppix's boot menu and in the GRUB I have on my hard drive's MBR.

The only other place where the power offs happen is MSI's BIOS flash utility. When you run it it presents a yes/no prompt. It had just displayed the prompt when it shut down. I dare not think of what would've happened if I had already said yes and it would've powered off while flashing the BIOS...

Hint, anyone?

First thing I would do is make sure the fan is working. Open the case and turn it on.
Is the fan working?

I haven't bought a boxed Intel processor in a while but sounds like you didn't attach the heatsink correctly. Unfortunately you can't just pop it off and try again. Every time the heatsink comes off you have to replace the thermal pad or reapply thermal paste. Air is an insulator, so a pocket or bubble between heatsink and CPU could easily produce the symptoms you describe.

A big Thank You for helping out! Everything is working now.

This problem was indeed a case of PEBKAC. I hadn't pressed the heatsink connectors deep enough and two of them were loose. I can be grateful that I didn't fry my CPU -- I was even stupid enough to compile gcc and g++ at 80 C before bothering to research the matter!

Properly reattaching the fan would surely have been enough, but I went and bought a Zalman CNPS9500LED. I don't regret spending the extra money, because this baby is practically noiseless and very efficient. I have the CPU and case fans set to minimum speed but the processor temps still won't climb above 35 C!