Hi Patrick!
This issue is being caused by a bug in the latest version of Outlook 2016, where messages downloaded from POP are deleted off the server or duplicated in Outlook. Take a look at our latest blog post for more information:
How Our Community Handled the Outlook 2016 POP3 Issue.
Hope this helps!
Andrea Free
SmarterTools Inc.
877-357-6278
www.smartertools.com