It's not connected to tweaker, apparently this has to do with the number of folders in myDocs exceeding a certain amount (23?). I remember reading in an earlier post about this bug. The solution was a little tedious (creating another folder and moving some around).
I have the same problem but i ignore it now. Hopefully this bug is fixed soon. When i see duplicate folders, the first instance is usually the actual one.
I remember reading that is has something to do with the number of files in those folders.
You would have to search for that post though or wait for someone more familiar with the issue to respond.
this has been discussed so many times before?
its a bug, fixed in PR1.2 (apparently!)
make sure everything in MyDocs is inside a folder and it goes away
works for me anyway