I've been trying to fix this problem for months and finally figured out what
my problem was.
I had rules directing all my incoming mail to folders other then my "Inbox".
When I deactivated all the rules, so that all my messages are received in my
"Inbox" and not specific folders, I no longer have the duplicate message
problem.
Also, I have heard that leaving message on your server after downloading
them to your Outlook, might be an issue. I do not leave any message on my
server, and never did, but always had this problem since I set up my account
this way.
Hope this solves your problems.