Flashing firmware or running certain utilities may require you to be in real DOS mode, but with some Windows versions it's easier said than done. Windows XP, ME and Windows 2000 don't give you this option readily, to say the least.
To make things simple, I suggest you download the:
Unzip and run it in Windows, it will prompt you to insert a floppy and will create a basic DR-DOS 7 boot-up diskette
Now copy the flashing file(s) to the floppy, and you are ready to go.
Boot the computer with it and run the utility directly from the A:\> prompt.
When the process is finished, remove the floppy and reboot.
Remark: The above DOS boot will not see your hard drives. If you need one that does, get FreeDos from this Etna's page, it supports FAT and FAT32 partitions.