Duplicate archive subfolders with Mail.app
I've had this problem for quite some time.  I did a completely new install on a brand new machine and still had this problem.  Here was my solution.

Back before Mail had an archiving feature, I had a folder called "Archive" that I used to put mail that matched certain rules.  The presence of this rule caused a folder to be created with that name.  This must have cause some electronic version of confusion.

When I removed the rule and deleted the folder one more time, I was left with a single Archive folder.