Operating System or Drivers
I think the problem has more to do with the operating system and/or drivers than it does with the flash drives themselves. I have a lenovo thinkpad with a built-in multi-card reader. I've hot-swapped the SD cards from my PDA to my laptop on several occasions. However, one time the card reader on the laptop said that none of the cards were formatted, yet when I put the card in the PDA it read all the data fine. One thing to check (if you're using windows) is the device manager. With device manager open plug a flash drive in and see if it shows it under there. If you don't see it try refreshing the device manager window or choosing the option to search for new hardware. In most cases the operating system (Windows) uses generic device drivers for hot-swappable flash drives. If you know the manufacturer of the drives you might try looking for more specific drivers however this may not make all the much difference.
*If I think of anything else I'll post it.