Hi, I have the latest firmware as of Jan 2013 and I've read the config files and I can confirm it's actually the factory setting that these fans are so loud and fast. Amazingly, the fans go up to 15,000 RPM and that incredible noise that sounds like an army of vacuum cleaners in your office is actually the fans only running at 50%. They go way lounder than that!
Anyhow, the solution is to change Intel's "SDR" settings. This is achieved by downloading Intel's latest SDR firmware update which is to be found on the support page for either your motherboard, system or chassis, and then editing the file containing the SDR settings before applying the update. For my motherboard - the S5400SF the file is called SF_11.SDR
This is not a simple undertaking in itself and it took me about 45 minutes to pick through the file. Once you get to grips with this file you will see that your fans are probably set to run at 50% even when the CPU is as low as 10 degrees Celsius. I changed mine to keep the fans at about 16% until the CPU reaches 30-40 celcius and only then do the fans start to climb to 50% and above.
The file contains a range of tables, all nicely commented which specify the various voltages and normal ranges of sensors, fans etc. which you need to ignore until you find "Temperature Fan Control Record". In here you will see a line as follows:
31 // Normal Control Value (31=PWM 49%)
The "31" is a 2 digit hex value to set the normal fan speed at 49%. I changed this to "10" so my normal fan speed is now 16%. I also reduced the "Sleep Control Value" from 64 to 32, i.e. 50%
Then there is a table of "Temperature/Control Value Pairs" and I reduced the first half of these, which represent temperatures below 40deg C down to 10 too - so my fan will not start to accelerate until the temperature reaches 40deg C.
The tricky bit is that these tables repeat throughout the file apparently one each for the five fans in my system and possible more according to different power profiles in use, however I just pasted the same values into each table. Please take care because in my file there were two different sizes of table, the larger started "0F //Count of temp/control pairs" and the smaller started "0D //Count..." so I had to make two versions of the table and paste the appropriate values into each table according to its record count.
GREAT CARE WAS NEEDED! I suspect an apparently minor typing error could potentially make the file either not work at all, or even worse, malfunction.
When I put the update with the modified .SDR file onto a USB and ran it as per Intel's instructions, lo and behold the fans span down to a level where I could take my headphones off. In fact it was quite quiet. However... I have yet to stress the processors so I'm completely unaware whether the higher values work and ramp up te fans when needed, or whether the processors / memory will melt!
IMPORTANT: I HAVEN'T A CLUE WHAT I'M DOING. CHANGING THESE SETTINGS CAN DESTROY YOUR SYSTEM SO THIS IS AN ACCOUNT OF WHAT I DID AND WHAT HAPPENED FOR ME PURELY IN CASE IT HELPS YOU. I AM NOT A PROFESSIONAL, THERE MAY BE HUGE ERRORS OR MISUNDERSTANDINGS IN THIS POST AND USE OF THIS INFORMATION IS ENTIRELY AT YOUR OWN RISK. However I hope it helps.