When you run the firmware update for BIOS/BMC/FRUSDR, it updates the fans (assuming they're plugged into the right spots).
Just follow the directions at http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=18039&ProdId=2600&lang=eng for all the updates
i am having the same problem with my S5520HC. I'm fairly certain all my fans are connected to the correct headers, i went into the intial setup and tryed all possible combinations of throttling modes pwm offsets and performance/ acoustics etc. which firmware EFI should i DL? is there a way to change the fan profile settings in the EFI shell? SIDENOTE: i dont have any operating system installed