On first sight, I'd say that your Windows installation for whatever reason (chipset, drivers, Windows or even something else) doesn't pass all commands required for flashing to the drive.
Binflash uses a certain command (actually more than one command) to identify the exact drive type. The official flashers just rely on the identification string as far as I know.
To me it looks like the commands Binflash uses to identify the drive fail as well as the commands that are used for actually transferring the new firmware from the internal RAM to the flash chips while the commands for erasing the flash still worked fine. This leads to the drive with just the bootcode but without a proper main firmware.
If you are unable to flash your drive under Windows in safe mode, DOS or Linux, you could try flashing your drive in a different PC.