If you have a flash drive that's not bootable because of how it looks to the operating system, try using BootIt to see if you can flip the Removable Media Bit. (Warning: It could theoretically damage your drive, so do that at your own risk.)
For the hackers:
Apparently it uses an undocumented/nonstandard SCSI opcode that some flash drives recognize (my Sony MicroVault and my Lexar JumpDrive certainly did) to flip their RMB. If I remember correctly, it's a 4-byte command whose first byte is 0xD2 (the opcode), whose second byte is 0x03 (no idea), and whose third byte is either 0 or 1 (0 for fixed, 1 for removable). The fourth byte has to do with something else (command control); it's usually zero.
So it's unlikely that it'll mess up the flash drive, because the flash drive should just return an error if it doesn't recognize the command. But since it's undocumented, it could be used for something else entirely (e.g. erasing the drive, updating some kind of information, or whatever) so there's a certain risk involved. Still, I'm pretty surprised that a Sony flash drive responded to a Lexar command -- it makes me think maybe it's not so nonstandard after all...