I used to get this problem when I used Vista. I found that it only occured when i removed my usb stick without going via the safely remove option (ie I just yanked it out). Try safely removing the drive and see if it stops bugging you.
I go through spells of not getting this message, but I never use the safely remove hardware, so there's no guarantee that will cure it. I think it's a timing issue - I must remove the stick at the wrong time.
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