A coworker of mine also had the same problem, then tried another system, this time going from version 40 to 99, and it worked. He was unable to recover from the one going from version 39 to 99 as well. So we need help to fix two units!
We've found a solution to the BIOS splash hang. After removing the Nvidia graphics card and booting to the onboard graphics, we were able to boot and upgrade to version 105. Once it was upgraded, we put the Nvidia card back in and everything worked!
I have the same issue. After removing the jumper, I get no display. I am stuck at the BIOS POST with the Intel logo.
Try clearing the CMOS first by removing all components, battery and jumper for about 20-30 minutes and then install the bios upgrade. Beside this step, as dhom mentioned, try disconnecting any video card before the update and if possible with a minimum configuration (1 Stick or RAM memory, 1 HDD).