Exactly as Juggy said. If your BIOS is reporting an A:, then Windows will detect it and install it. Disabling it in Windows is pointless. Make sure it is disabled in your BIOS. But even that is unnecessary. If you want to boot off of a USB device, then just set your BIOS to boot off USB device. Setting it to boot off your A:, and expecting it to boot off a flash disk is silly, as it is two VERY different technologies, which do two different things. It won't in a million years work, even if you pray very hard.
Basically, to disable it showing in Windows, disable floppies in BIOS. However, some builds of XP and Win2K by default show a A:, even if not present. I have queried with MS, and they say it is occasional, and often due to third party app's reloading a system DLL which creates the functionality for their software. So they say it is not their issue.
PS, this is not an official MS stance, but heresay from talking to employees.