I have a new build s5520sc mb in an intel chassis runining xp x64 sp2. The system status led blinks amber very early in the boot sequence, before windows begins to load. How can I determine the cause? Everything seems to work ok. I have substituted the standard chassis fans for noctura low noise ones; otherwise, everything is standard.
First make sure you apply latest http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&ProdId=3073&DwnldID=18127&lang=eng BIOS/Firmware. After the update if you're still seeing same issue then you may need to use the SELviewer tool to read the System Event Log to identify the error.
Since you mentioned you replaced fans with low noise ones, this could cause amber LED if the fans are running slower than threshold and BMC thinks the fan is not working properly. Actually when using an Inter chassis with proper settings the noise level should be quite low on this system.