Are you syncing Wireless or via desktop?
Wireless Notes syncing (thru a BES Server) uses the R6 inotes design. In other words, if you look at your notes mailfile via a PC IE browser do you see duplicates as well?
If you don't know how to view your R6 mailfile via a browser you may want to ask your companies Notes Admin.
If this isn't about wireless syncing, then just ignore