I put together a system with a Core 2 Quad Q6600 CPU and a Gigabyte GA-P35-DS3L motherboard and am experiencing problems with the HSF. Short version: The fan currently tries to spin on power on, but then stops, then tries to start again, but then stops again. Meanwhile, the CPU temperature alarm is wailing. Long version: When I went to power it on for the first time, it went through the normal post, etc, and ended up at the screen saying insert boot disc (as expected). However, it then spontaneously shut off. Suspecting heat issues, I waited a bit (so it might cool off if it was heat), then booted and went into the BIOS. I looked at the CPU temp and it was at 100 C! I quickly turned on the CPU temperature alarm to alarm at 70C and then turned the computer off. I then tried reseating the HSF, making sure it was properly seated (with the HSF prong things properly going through the motherboard holes). This time, when I powered up, the fan initially didn’t spin, and the temperature alarm started going. But then the fan started up and kept going, turning off the temperature alarm. This happened while I again powered up after installing the DVD drive and hard drive, but I was able to install windows and boot into that with no problems. However, the next day, I encountered a problem where the CPU temperature alarm wouldn’t deactivate after booting, even though the post was normal. After putting the case on its side and booting (as well as fiddling one last time with the HSF), I got the computer to boot as before (when the alarm quickly turned off, as described above). Later, though, the computer again booted to the continuous temperature alarm. I watched the fan while powering on and it looked like it started to go, but then stopped, and then started again, and then stopped again. So, my question is this: Is this a defective HSF? Or could this be a problem with the motherboard? Any help would be greatly appreciated!

It really just sounds like the BIOS is being stupid about fan control. Just connect the fan to a regular power connector to bypass that.

Ah yes. Thank you both! I tried plugging the CPU fan into a system fan plug and it spun up at start-up (along with the CPU fan fail alarm!). I then disabled the auto fan control in the BIOS and reconnected the fan to the CPU fan plug, and everything seems to be working fine.

Thanks again!