Have you looked through your complete client list in your database to make sure there aren't some duplicates lurking outside of the 1065 module?

Yes, each one it is happening to is a new client

Either paper file or call support - I'm not sure what is happening if you are dealing with new clients.

So if the paper file extension is postmarked today they will accept it as filed on time, correct?

Correct

If these are new clients to your business, could it be possible that the client's previous preparer has filed an extension for the client ?     

Wouldn't that be a plain old rejection notice though?

I interpreted the duplicate to mean that a Rejection was received stating there was a previously accepted extension.  

Was the DUPLICATE in the  Pending Tab of EF Center   ?