You shouldn't be running a bios flash-update from within Windows so the operating system is irrelevant. A DOS box or Command Prompt launched from the Start menu is still Windows. You need to boot from a floppy boot disk and work from that. click here and click here for guides on how to do it.
It is unwise to flash your bios unless you have a pressing reason to do so as there is always a risk of ending up with a useless motherboard if something goes wrong. If you do proceed then read all instructions carefully and pay attention to all warnings.