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Why does Outlook keep Downloading Duplicate Messages?

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1) Outlook downloads messages from the POP3 server twice

Outlook downloads messages from a Post Office Protocol 3 (POP3) 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 on the POP3 account.
This problem occurs because a background synchronization took place at the same time, or just after the Deleted Items folder was emptied. This is an issue with the order in which Outlook carries out the deletion from the server and the downloading of messages.
There is no available workaround for this problem other than not to begin a synchronization at about the same time that the Deleted Items folder is emptied. This issue does not result in data loss (other than messages that you instructed Outlook to delete). Simply delete the duplicate messages.

2) You are prompted for your password, and you may receive duplicate e-mail messages if your profile has two POP3 accounts in Outlook
When you log on to Microsoft Outlook by using a profile that contains two Post Office Protocol (POP3) accounts, you may be prompted to provide a password for one of the accounts, and you may receive duplicate e-mail messages from the accounts.
This behavior can occur if your Outlook profile contains two Internet accounts that both point to the same POP3 server.
To resolve this issue, turn off e-mail reception for one of the POP3 accounts:
  1. Go Outlook → Tools → Send/Receive Settings → click Define Send/Receive Groups.
  2. Double-click the group that contains the two POP3 accounts, and under Accounts, click one of the POP3 accounts.
  3. Click to clear the Receive mail items check box.

3) POP3 Headers Are Duplicated
If you press the F9 key while you are online to synchronize your Microsoft Exchange mailbox with your offline folder (.ost) file, the headers from your Post Office Protocol version 3 (POP3) account appear to download twice.
This problem occurs because your message headers from the POP3 account are placed in the .ost file with the message from your Exchange server account when you download them while you are working offline. When you go online and press the F9 key to synchronize your accounts, the headers from the POP3 account are downloaded and the changes in the Exchange account, including the downloaded POP3 headers in the .ost file, are also brought down giving you doubled POP3 message headers in your online Inbox.

To resolve this problem, enable the Download complete item including attachments option in the POP3 account. To do this:
  1. Go Outlook → Tools → Send/Receive Settings → click Define Send/Receive Groups.
  2. Click to select the group name, and then click Edit.
  3. Under Accounts, click to select the POP3 account.
  4. Click Download complete Item including attachments.
  5. Click OK, and then click Close.

4) Anti-Virus Software
Many of the anti-virus programs that scan email can cause this issue as well. When the messages are large, the software can cause a 'timeout' to the server before it sends back a flag that identifies the message as being read. As a result you will receive the message over and over.
The easiest and fastest solution to the above problem is to log-in to
the mail server and delete your mail message that is causing the
problem - or all of them for a fresh start. (NOTE: Please make sure
that you have downloaded all your messages first)

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