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There is a bug in WF-Downloads where if you specify that only certain groups can submit files, that only affects the Submit link in the main menu, it doesn't affect the Submit link in the main page of the module. And the form also does not check to see if the user is allowed to submit, so anyone can submit files regardless of your group selection.
We have made a patch that addresses that, details are here:
http://sourceforge.net/tracker/index.php?func=detail&aid=1149489&group_id=113004&atid=663913
--Julian