Mac OS X 10.2.8 or earlier: Mail message duplicates itself in the In mailbox

Resolution

1. In Mail, choose Mail > Preferences.
2. Click Rules.
3. Edit each rule other than the rules "News From Apple" and "Junk." Look in each rule for action under "Perform the following actions" that includes "Transfer Message, to mailbox: In" (or a custom mailbox within In).
4. If you find this action, change that part of the rule so that the message is directed to a different mailbox--one that is not the In mailbox or within the In mailbox.
   
   Note: If the rules "News From Apple" or "Junk" were previously customized, you should check them for these actions as well. 
    

If the issue persists, use these steps:

1. Quit Mail.
2. Click the Finder icon in the Dock.
3. Choose File > Find.
4. Type:
   MessageSorting.plist
   
5. Click Search. The Search Results window appears.
6. Click the file named "MessageSorting.plist". The filename should be selected, allowing you to change it.
7. Type:
   MessageSorting.plist.old
   
8. Press Return.
9. Close the Search Results window.
10. Open Mail.
11. Delete the unwanted duplicate messages.