I'm running an Intel E8400 with an Asus P5Q P45 mobo. My case is a Coolmaster Centurian. I drilled out holes for an additional (third) vent on the side panel, and put an 80mm and 120mm fans over 2 of the vents blowing directly onto the mobo. So in total I have an: 80mm fan intake in the front, 80mm and 120mm intake fans on the side blowing on the mobo, a 120mm fan exhaust out the back, and 2 open air vents in the side and back, and the stock heatsink and fan from Intel.

I would call this overkill cooling, considering I have done NO overclocking or adjustuments to the BIOS settings whatsoever. Was considering it down the road, but this is a brand new PC and I want to get everything running tip top first.

I installed Vista and starting doing the OS updates, getting drivers, etc today. Upon a restart I got a CPU Overheating warning and went to the BIOS to check the temp. IT WAS AT 90ºC!!! Of course I immediately shutdown to investigate. I checked out my heatsink, it was securely on the cpu. I removed it and saw that the thermal compound on it wasn't very well spread and had gotten quite hard, so I cleaned everything with some isopropyl and put on a nice thin coating of my own silver thermal compound.

That didn't help. I turned on my pc again (after waiting quite a while for it to cool down) and went straight to the BIOS. The temp was already at 55ºC at startup, and I just sat and watched in BIOS and it just kept climbing and climbing, by the time it started getting over 70º I just shutdown and hopped on the forums on my old rig.

What the hell could be going on?

your heatsink is on wrong, duh.
maybe you have to twist the hs so it doesn't set on the capacitors by the socket. happened to me.

When I was installing my e6750 I had such huge temps.
It was due to porly installed cooler, it seemed really well
sitting from the outside but apparently it wasn't. After re-installing the cooler it was working just fine, 30 C.