Hello,
Have you tried a different BIOS update method (such as F7 or Recovery)?
BIOS update instructions
http://www.intel.com/support/motherboards/desktop/sb/cs-022312.htm
Please bear in mind that is strongly suggested to update the BIOS incrementally. You may also remove the power and CMOS battery for 20 minutes before your next attempt.
In case the issue persists, is there a message or error when you attempt to update before Windows* starts?