Duplicate Mail Archive folders "ON MY MAC"

I recently migrated all my email over to Mail from the fast-deprecating M'soft Entourage. Recently, I have been trying to diagnose and fix an issue in Mail 7.0 having to do with the automatic Archive command. When the command is applied to an iCloud message, then it is archived in the iCloud [myicloudusername] folder under Archive under the MAILBOXES section, which I think is logical and correct.
However, when applying this command to any email other than an iCloud email, the message is archived in 9 (nine) duplicate folders, each titled "ON MY MAC" in the MAILBOXES section and under Archive. This syndrome seems to bw widespread among Mail users, with the main difference being the number of duplicate folders. Selecting one of these folders and deleting it causes all of the ON MY MAC folders and their contents to be deleted. This is a forever deletion; nothing goes to Trash.
Inspecting the ~/Library/Mail folder I find that an Archive.mbox appears as a subfolder of Mailboxes. Appearing there are all of the non-iCloud Archived messages as would be expected. There is no hint of multiple instances of this and nothing named "ON MY MAC" anywhere therein.
This problem was first observed in I think, Snow Leopard or Lion. I have not seen a reliable solution or an explanation for it. Other than the multiple ON MY MAC instances under Archive under MAILBOXES, the issue seems benign. However, just to be extra safe, I have decided to drag messages out of lthe ON MY MAC folder(s) from time to time and into a folder which I have called "Archive - Local" under the sidebar section also called ON MY MAC. That way I still enjoy the automated Archive command. I can keep the multiple ON MY MAC folders hidden with the triangle control next to the Archive folder.
Still, this is annoying and I am a bit squeamish about issues like this in mission critical applications such as Mail. Is this just a display bug or a structural/database issue? I am writing here to find out if anyone has found a solution or explanation for this, or if it's just another bug that Apple has been kicking down the road for awhile. Any bits o' wisdom out there?

More or less the same issue here. I have three "On My Mac" subfolders under "Archive". I think they are the same physical folder because deleting a messgage from one deletes it from all three. Previously I could drag a message on the "Archive" folder and all three subfolders would update. With the Marvericks update 10.9.1 I have to drag onto the last of the three subfolders. So looks like Apple touched the code but just made the problem slightly worse. Like you, I hate having flaky behavior in such an important application.

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