Let me add a bit more information, I've had this computer for almost 2-3 years now.
The fan ran perfectly, cooing like a baby. Then just randomly, out of nowhere this issue arises.
Now in my old fan, did the 3pin connector also control the speed of the fan? And if not, then why was it always running at a slow rpm, similar to a Smart fan controller.
Could it be possibly that a bit of circuitry is fried? And that part specifically is related to the CPU controller.
Also the BIOS is a 100% locked down BIOS, you cannot adjust anything in there aside from the time, boot preferences, very standard stuff.