As mentioned here:
http://forum.mailenable.com/viewtopic.php?f=11&t=41869
Just updated to the latest version of server and plug in on Office 2016, and still seeing this behavior.
The duplicates go away each time I "reset from server" but they come back within a day.
These are only artifacts of some kind, not actually duplicated messages on the server, they only appear in Outlook and must have something to do with the indexes between the server and client not synching properly.