If reloading the bios (from Intel) and reloading the Intel active monitor application does not fix it,
You probably do have a bunk fan or a bunk motherboard.
There is a regulator circuit on the board that speeds up the fan according to the temperature. It could be FUBAR.
It sounds to me like Intel(R) QST thinks that a fan is stalled and it trying to start it operating. I would suggest that you go into BIOS Setup and change the redetect fans parameter setting to "Next Boot". After rebooting, the fan speed will stabilize if this is the issue...