Some mobo's have the option to flash on the mobo, think mine says press f10 for flash menu or something on startup (takes the bios from usb mass storage). I just did that to flash my current mobo.
Windows flash is defo not a good idea. Loads of folks that have used this metheod have screwed things up and run into all sorts of probs. Personally, i just download an .iso of the bios, burn to cd, then in my bios during post, i have the options of del for bios, esc for boot and alt+f2 for flash...Obvious one here then select the .bin file from disc if it doesnt do it automatically. p.s. make sure you're system is stable 1st as if it hangs during flash, its a new bios chip.....