actually, BIOS updates are not scary in my opinion on FSC business PCs. The BIOS update cannot go wrong from software side (like wrong BIOS - this is checked by the software), so the only issue you could get (even if there is a power failure during flash, etc) would be in the unlikely event of the hardware being damaged (flash chip broken).
Unlike "normal" (China/Taiwan) boards, the boards in business PCs from FSC (and other big brands) are quite safe to flash. Even if anything should go wrong, you can still do a BIOS recovery with a CD, USB stick, diskette, etc.
The easiest is to use deskflash under windows. Download the respective BIOS update file for desk flash plus the utility:
http://support.fujitsu-siemens.com/Down ... AD7C1A95BD
The process should be self explanatory.
But to be honest, I don't know if this would help with your issue. I have heard about issues with WD vs. the Nvidia chipsets. So if you can still exchange the harddisk maybe get an other type like Maxtor or Seagate.