I'll start at the beginning.

Last week I was adding a USB card when, out of curiosity, I pulled the CMOS jumper off. Somehow, I managed to put it back on wrong and when I put everything back together, naturally, it wouldn't boot. So, I opened it up, correctly mounted the jumper, and rebooted.

Now my CPU fan seems to have a mind of its own, and I'm wondering if I may have caused any damage to either the fan or the motherboard by trying to boot the computer with the jumper mounted incorrectly.

As far as I can tell, everything else seems to be running fine. In fact, if it wasn't so loud I wouldn't be concerned, because my hard drives are running at least 10C cooler now. Problem is, the noise drives me crazy.

When I boot, the fan runs quietly for the first five minutes or so. Then for about the next five minutes, the speed gradually increases to a high RPM.  For the next half hour it runs at high speed. Then it slows down and starts oscillating from high to low, which it continues to do from then on.

I thought I may have corrupted something in the BIOS, so I tried re-flashing it to the latest version, but it didn't help. I've already taken the heat sink out and cleaned it; it wasn't even clogged in the first place.

Is there anything I can do? Would replacing the fan solve my problem, or would it be a motherboard issue?
Any suggestions would be greatly appreciated...