Question: I have been receiving two copies of email messages in Outlook when I check for new mail. What is going on and how do I fix it?
Answer: This issue is quite common and is caused by a wide variety of issues. Here is a quick rundown of the problems and what to do to fix them (Note: This issue effects both Outlook and Outlook Express, for the remainder of this article both will be referred as 'Outlook'.):

1. Outlook does not properly track that it has downloaded a message when leave a copy of messages on the server is selected. Often, though not always, caused by a corrupted message on the server.
a. Start Outlook.
b. Click on 'Tools' -> 'Accounts' (or 'Tools' -> 'Services').
c. Select the 'Mail' tab, click on the problem mail account and click 'Properties'.
d. Select the 'Advanced' tab and uncheck 'Leave a copy of messages on server'. Click 'Apply' and then 'OK'.
e. Close the Accounts screen.
f. Press 'Send/Receive'. This will check your messages and remove all old messages from the server – including any corrupted messages. Either send yourself a test message or wait for new mail to arrive to see if Outlook is now working correctly. If it works, you can try turning 'Leave a copy of messages on server' back on. If the problem reappears, turn 'Leave a copy of messages on server' off permanently. If this does not work, continue through the additional solutions below.

2. Outlook downloads messages from a server again after it empties the 'Deleted Items' folder even if you have both the 'Leave a copy of messages on the server' and the 'Remove from server when deleted from Deleted Items options enabled'. This problem occurs because new messages are downloaded at the same time or just after the Deleted Items folder was emptied.
a. This is an issue with the order in which Outlook deletes and downloads items from the server. The only way to keep this from happening is to not delete messages from the 'Deleted Items' when downloading new messages from the server.

3. If exchange server is used with your online mail server, the Exchange mailbox (your default delivery location) cannot properly keep track of which POP3 messages have already been downloaded when it is offline. Outlook performs a second download of the email messages if the POP3 account is configured to leave a copy of messages on the server.
a. The Exchange server needs to be brought back online.
b. If your Exchange server is down often, you can fix the problem by changing your default storage to your local computer. (Though this will remove Exchange functionally – archive, backups, etc. – from the account.)

4. If you use mail filtering – such as Outlooks mail processing rules or external processors such as Spambayes – for your messages, the filter could be re-sending the messages to your account.
a. Check your message rules and any external mail filters to see if they are sending (or CCing) messages to your account. If so, be sure to disable the functionality by following the instructions with the filtering program.

5. A corrupted Outlook Express (not Outlook) data files do not properly track downloaded messages when leaving a copy of message on the server. Since it does not know that it has downloaded the messages the first time, it re-downloads them a second time.
a. To fix this, find the location of your Outlook Express data files. This can usually be done through either 'Accounts' or 'Services' in the 'Tools' menu of Outlook.
b. Once you have the folder location of the of the Outlook Express data files, shutdown the program. You will then need to go to the data file folder and rename all pop3*.* files to pop3*.bak files. This will make backup copies of the corrupted files.
c. Restart the computer and start Outlook Express. This will create new pop3*.* files and should fix the problem. (Note: All files still on the server will be downloaded one more time. After this initial download, you should no longer receive copies.)

6. If you are receiving duplicate messages and receiving an error from Outlook that the message download is not completing successfully, you have a message on the server that is either infected with virus or too large to download without timing out.

7. If all of the above have failed, the final fix should be the following:
a. Go into Outlook, click on 'Tools' -> 'Accounts' (or 'Tools' -> 'Services') and select the problem account. Press the 'Remove' or 'Delete' button to remove the account.
b. After this is done, restart the computer.
c. Start Outlook, go to 'Tools' -> 'Accounts' and re-add the account with the information provided by your service provider.