Brian,
What version of MC do you have? If not, 10.0.116, please get that one. If you are seeing a message about duplicates prior to the start of the sync, it is not referring to duplicates on the Zen, but duplicates in MC based on a match of Name, Artist, Album, Genre and Track Number information. MC will not resend files that are already on the Zen. However, MC allows you to have multiple files with the same Name, Artist, Album, Genrem and Track Number and we do not allow that on the Zen. If you are going to send 'All files' it would be best if you resolved these duplicates. Or, don't use send all files and create playlists/smartlists with the files you want to send.
Steve