If you look at the ASUS forums, the experienced members there will tell you to avoid the in-OS BIOS update.
The EZ Flash utility can be done from the BIOS,
save the bios file to the flash drive (formatted to FAT / FAT32, not NTFS), name it something like
P5E.rom
(replace P5E with your mobo's model)
then reboot, enter bios, choose EZ FLASH utility, then pick your bios file and update from there.
It is also not recommended to use "Alt-F2 on boot" to flash.
I believe the reason for all of this is that doing it from the bios minimizes the chance that something can go wrong and leave you with a FUBAR bios.
You can also do this from a bootable floppy (DOS method) or even a CD-R (EZ flash method, I believe)