This happens when you mix wu-imap and vm-pop3d in with the same inbox (ie: if you use squirrelmail, and outlook with pop).. and have also set outlook to leave the message on the server.
wu-imap adds message headers to the emails when you view them, which changes the email headers.
Outlook relies on the headers being unchanged to indentify if it's already seen that message.
Since wu-imap changes the headers, outlook thinks it's a new message and downloads it/shows it to you again as a seperate message.
With the "leave message on server" option for pop in outlook, wu-imap is free to change the headers again if you login to squirrelmail, so with pop/outlook, you'll get yet another copy.
Solution 1: use only pop (/webmail), OR only imap (/squirrelmail). Note: outlook does support imap instead of pop.
Solution 2: upgrade to dovecot, as it's one program that manages both pop and imap, and the issue doesn't affect it.