Try Process Explorer:
http://technet.microsoft.com/en-us/sysinternals/bb896653.aspxThat will list all running processes. Within the Procmon application, select
Find -> Find Handle or DLL. You can then search for open handles on the USB drive, which should lead you to the offending application. (You may also be able to force the handle closed by right clicking on it; this can cause system instability.)