I have a strange problem with Mail and I cannot understand if it's a bug or not.
When I archive a message, Mail creates duplicated subfolders. They are called "On my Mac" and they are located under "Archive" folder.
All the subfolders, 4 in my case, contain the same message. This is quit strange since if I delete a folder, I cannot find the message anywhere else (i.e. the message is deleted in the other ones).
Here a discussion on Apple forum where it appears to be an unresolved bug: Duplicate Mail archive folders.
I'm running ML 10.8.4 and Mail 6.5.