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If you have a USB drive , AND the drive is open in Explorer, then that drive is in use and can not be removed. You have to close the Explorer session on the drive before you can safely remove it.
Cameras that are open in Explorer will behave the same way. A camera that is open in a photo editor is also in use and cannot be removed.
I've never seen the problem of a USB device that is being used and I can't figure out by what. I get the Device In Use error, but the device is always in use by something that I've forgotten to shut down first. If the device is bootable, and you booted to it, then by definition it is in use and can't be removed.
Get a copy of "Process Explorer".
http://technet.microsoft.com/en-us/s.../bb896653.aspx
Start the program, then go to "Find". In "Handle or DLL Substring", enter "C:" without the quotes. By doing that, you might get to see the dependencies on your boot drive. (The returned list should be very large, and not all items will make a lot of sense.)
Now, try another search, only this time, use the drive letter of your flash drive. Is anything returned in a search ?
try going into My Computer, right clicking on the drive and click "eject"