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I recently built a new system. I have had basically no problems with it in the temperature department--VGA was pretty cool, CPU was between 38-47 depending on load, but the Northbridge was too hot to touch. So I bought a dedicated Northbridge fan/sink from Coolermaster (thank you Gigabyte for only including passive cooling). I installed the thing, and plugged it into the sys fan space on the motherboard.
When I started up the computer again, however, the bios alarm started going off, and the thing shut down when loading windows. I tried again, and this time managed to rush into the BIOS and check the PC Health numbers. There was my CPU, of all things, shooting up from 62 to 65 to 70 to 72 to shutdown...
Can anyone think of any reason why this might be happening? The thing CPU doesn't even feel hot to touch. All fans are spinning properly. How can it be that installing a NEW fan has increased CPU temperatures by 25C, to the point of not allowing me to start up my computer?
My setup is:
MOBO: Gigabyte 8N-SLI rev1.1 (nForce 4 SLI intel chipset)
RAM: 2gb Corsair DDR2 667
VGA: MSI GeForce 7900GT
CPU: Pentium D 940 (factory clocked, stock cooled)
PSU: Antec TruPower 430

You know what they say..."if it aint broke, don't fix it". If you weren't having any problems, the NB obviously wasn't too hot. GigaByte has an optional fan for the NB:
http://www.tweaktown.com/popImg.php?img=8nslil_2.JPG
My guess is you disturbed the CPU HSF when you were playing with the NB & it's no longer seated properly on the CPU.

I think Jam is right.
If the heatsink is not hot, that means the heat transfer from the CPU to the heatsink has been disrupted.Do yourself a favor BACKUP!

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