Just a wild guess here... Download MainMenu (correct spelling for google), install it, launch it (it appears in the menubar above) and ask for Show Invisibles in the Finder section. You will see plenty of files everywhere but never mind about that for now: see if by doubleclicking on your external hard drive, if you wouldn't see the files in a folder that should now show up called .trashes.
Other than that, I have no idea.
To make the invisible files go back to being invisible, just click on Hide Invisibles.