There are a couple of situations which may cause Outlook to download duplicate messages:
1. Outlook Downloads Messages from a POP3 Server Twice
http://support.microsoft.com/default.aspx?scid=kb;en-us;292249
2. Mail Retrieval Problems Occur When You Receive POP Mail
http://support.microsoft.com/default.aspx?scid=kb;en-us;317945
3. Password Prompt, Duplicate Messages Appear If Outlook Profile Has Two POP3 Accounts
http://support.microsoft.com/default.aspx?scid=kb;en-us;284404&Product=ol2002
4. POP3 Headers Are Duplicated
http://support.microsoft.com/default.aspx?scid=kb;en-us;289942&Product=ol2002
Other tips to prevent duplicate emails:
1. Download and install the latest Microsoft Office Service Pack and Patches.
This is most easily done by accessing the link to Office Update from, http://windowsupdate.microsoft.com
2. Increase your server timeout settings to 10 minutes:
Tools|E-mail accounts
View or change existing e-mail accounts
Select the account corresponding to your domain account
Click the Change button.
E-mail Accounts
More Settings
Internet E-mail Settings
Outgoing Server
Server Timeouts (Increase from 1 minute to 10 minutes)
3. Empty the Deleted Items folder only when Outlook is not checking e-mail in the background.
4. Configure Outlook so as not to check e-mail more frequently than ten minutes.
5. Configure Outlook to download complete Item including attachments.
Tools|Send/Receive settings
Define Send/Receive groups.
Click to select the group name, and then click Edit.
Under Accounts, click to select the POP3 account.
Download complete Item including attachments.