Microsoft broke the POP3 handling in February, pertaining to the leave copy on the server option. When this is enabled Outlook downloads all emails on the server regardless of whether it has already downloaded them in a previous session.
Apparently it's been fixed in the click to run edition, however my non click to run Outlook 2016 Professional is still having the problem. Version 16.0.4456.1003.
I have the web interface open so when Outlook has downloaded the emails I delete them from there, but after ensuring my other computer has them download also.
This is driving me potty, click to run was fixed why not non click to run?