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Remove the account. Reboot. Add the account back.
From their HELP section: Why am I still getting duplicates of POP messages in my Inbox?
If you chose to leave POP e-mail on the server when you set up your POP account, and you also chose to download all messages to Hotmail, all messages in your POP account are copied into your Hotmail account every time you check for POP e-mail. To stop seeing the same POP messages repeatedly, follow these steps:
On the Options page, click POP Mail Retrieval Settings under Additional Options.
Select the Download new messages only check box for each POP account you have, and then click OK.
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