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Details of the components might be useful: Board = DQ67EP, CPU = Xeon E3 1235, PSU = FSP Aurum 400, RAM = 2 * 4GB Samsung 10600U, Belkin Flip KVM.
I understand you are having problems with the motherboard and let me help you.
All the information you have provided is very helpful and based on that I also think that the issue can be the motherboard.
There are just some steps I would like you to try:
1. Make sure the heat sink fan is connected to the CPU fan and not the rear fan.
2. Power cycle the unit by removing all components from the motherboard and the battery for about 20-30 minutes.
3. Try reseating the BIOS settings to default by pressing F9.
You probably did these steps but just in case try them again. If you add more thermal paste and issue persists, there may be an issue with the board chipset and a replacement may be needed.