Are you flashing from a floppy disk in DOS mode or from within Windows??
If you are flashing from the floppy disk in DOS mode then your Windows settings will have no affect on the procedure. If you are overclocking then all you have to do is set the cpu to it's default speeds, you don't have to change the voltages or any of the other settings (or that's how I do it).
If your flashing from within Windows then your Windows settings will matter. Once again , in the bios, set your cpu to its default speeds and leave all your other settings alone. Boot back into Windows and I would disable your Anti-Virus, Windows Update, Steam, MSN Chat, Outlook or any other program that can perform tasks independently. Then I would perform the Flash.
Never Flash your Bios when there's a chance of Losing Power, as in, Storms or in periods of High Electrical use if brown-outs are possible.
Edit: I started typing this and then a friend came over and by the time I finished you were done.