I've seen that behavior on and off with some of the machines here at the office (a pool of about 30 machines). We use a POP3 server. It seems to come and go, and I have no solid answer on how to prevent it from happening. I've been teaching the users affected to use the 'View\Arrange By\Current View\Unread Messages in this Folder' menu choice to help them delete duplicates of messages already read.
This issue is a real PITA if you have any dial-up users with big mailboxes.
-Zeke
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WWFSMD?