Windows is an unstable mess when it comes to dealing with drives. You got an OS that sends messages to the drives polling it at regular intervals, you have background programs that interact with the drive, etc. It's like performing surgery in the middle of a busy street. Flashing in Windows is the number one cause of firmware misflashes, which is why a number of manufacturers require that firmwares be flashed in DOS.
@The Doom Master
See the link I provided above about creating a boot disk that is designed specifically for firmware flashing. Use that. As for the rest, follow the instructions provided by the manufacturer as this varies from drive to drive.