Ok I have just built this server with the following:
Intel S5000VSA Motherboard
Intel SC5299DP Chassis
I was having some very noisy fan issues so I ran through all of the steps in this article to fix the problem. http://www.intel.com/cd/channel/reseller/apac/eng/products/server/250740.htm
After the FRU/SDR update the problem with the fans stopped.
The fan issue is now resolved however I still have 1 more issue that is causing the amber light on the front of the server to blink. I used the SEL Viewer to lookup what might be causing this and I don't understand what the error message means or what to do to fix it. I have found a few suggestions online to update the FRU/SDR again but I already did this and this is how I fixed the fan problem. I looked through the BIOS and can't seem to find anything either.
In the SEL it is listed as a CRITICAL EVENT and I have pasted the error as follows:
Num : 1736
Time Stamp : 01/05/2010-18:58:36
Sensor Type & Number : Voltage /BB +1.2V Vtt (#0x10)
Event Description : CRITICAL event: BB +1.2V Vtt reports the sensor is in a low, critical, and going lower state. Sensor reading: 1.0962 Volts. Threshold value: 1.0962 Volts.
Generator ID : BMC - LUN #0 (Channel #00h)