yeah i am alos having this same problem but my problem is different one. Would anyone know why a CPU fan would stop running. I removed the fan from the heat sink and tested it on a different motherboard. It worked fine. I suspect my current motherboard and maybe some BIOS settings may be disable but I don't know where and what to look for next.
Answer to first problem. Buy a new fan and soon! it sounds suspiciously like you are cooking the Processor! And suck the dust out of the system. Power the system off and use a vaccum cleaner/airduster areosol.
Answer to Hijack above,It's the pins on the board that have failed look for the pin outs marked sysfan on the board, you may find these are still operational. The problem you may encounter from here, is that some systems may not boot as the system cannot detect the fan.