If you have a large amount of mail, store copies of it on the server and have Outlook check for new mail every few minutes, there's a good chance you will get duplicate email. Outlook will never complete a check mail pass before the next one starts, this prevents Outlook from marking the mail as downloaded. Try extending the time interval that Outlook checks for mail:
- Click File > Options > Advanced.
- Scroll down to the Send/Receive section and click Send/Receive.
- Set the time interval for "Schedule an automatic send/receive every" XX Minutes to 15 minutes or more. A very large amount of mail on the server may require more time (Screen shot for this step is listed below).