At times, POP severs can act funny and can send two copies of the same maiL To remove duplicates of the same mail, The Bat! has a ready-made feature:

Name:  Automatically Deleting Duplicate Messages.jpg
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1. Click on the Inbox, or on the folder where you have multiple messages, and then from the main menu select Folder.

2. Under Folder, select Remove duplicates and that should do it alL