When you run a BIOS update utility in Windows, It applies the data when the computer reboots- so yep, when you reboot.
Unfortunately, even the correct BIOS updates can go wrong, due to several reasons: corrupt BIOS update file or simply an error during the writing of BIOS data.
I once updated a BIOS for a Compaq OEM Asus A7N8X-LX Motherboard- AMI BIOS, with success. Did the same update for my own Compaq OEM Asus A7N8X-LX Motherboard- AMI BIOS of the same version, and when it rebooted afterwards...it never booted again. Same problem, lights, fans etc...but no activity. Fortunately, I was still under warranty with Compaq, so I simply had to send it off and the motherboard was replaced for free.
Just as Nubius said, you could get your BIOS chip hot-flashed, or simply re-flashed. http://www.badflash.com/
can offer this service for a small fee.