The ability to update the BIOS while Windows is running is a very new trick. I'm not trying to offend you but if you think back just a few years such updates were done with DOS boot diskettes for years and arcane command lines.
It's improved but I have no qualms with a boot CD or diskette to do this update.
I have Windows 7 Ultimate 64-bit with a GA-EP45-UD3P (Rev 1.0/1.1) motherboard. When I play games I get a BSOD STOP 0x0000001E. It occurred to me I didn't install all my drivers or the new BIOS for my system since updating to Windows 7 64-bit. I have installed all current hardware drivers, but when I try to install the BIOS it says it is not compatible with 64-bit and to contact the company. I have contacted them, but without a reply. Is windows just saying it isn't compatible when I try to run the update in windows, but really is compatible if I used a disk to update the bios?