Apparently, if you’re running an Intel 5000-series motherboard in a non-Intel case, the fans shall run at 100% RPM, unless something called an SDR file is custom-written. See:
http://www.intel.com/support/motherboards/server/s3420gp/sb/CS-031016.htm
and quoted:
Thermal Test Level:
Intel performs system level thermal testing of a given Intel Server Board in all listed 3rd party reference chassis. The server board is configured to use a generic fan control scheme which operates all attached system fans at 100% pulse width modulation (PWM). The generic fan control scheme is set by selecting the “OTHER CHASSIS” option using the FRUSDR Configuration Utility.
If info on creating an SDR file becomes available to me, it will be posted!
Also see this Intel forum for more information.