I have wrestled with the "LOUD FANS" problem in two different installations. One installation was a rackmount intel chassis/intel S1200 motherboard. The other was a pedestal intel chassis/intel S2600 motherboard. There have been multiple incidents between the two installations that I manage. Across these incidents, I have quieted the fans with 3 different actions:
1- total powerdown/go dark. Remove redundant power supply modules, count to 43(or maybe it was 44, you get the idea) replug power supply modules and go to town.
2- rewrite of BIOS/FRU/SDR/ME- this is an intel recommendation...upgrade of BIOS/FRU/SDR/ME or, if you're already on the latest, rewrite them.
3- OK, this is the one that got me tonight. I go to a job to upgrade RAM, I do my thing and the fans go nuts- LOUD like you're at the airport! Well, guess what? I hadn't replaced the stupid cover on the pedestal chassis! There are "contacts" there, and when I replaced the cover, everything settled down!
Just thought I would send this along in case anyone has encountered what I have encountered and then tried to find direction.