I had the same issue. There is probably a simpler was of doing it but I deleted the contents of the saved variables folder (where addon info is saved) on each account and redid my UI on each toon.

However, I now run all my clones and my main from 1 wow folder (with a seprate wow folder for when I'm not multiboxing) and I have not had any issues with lag or anything and since bindings are saved per character (assuming you check the 'character specific only' box in bongos' bindings page) they all retain thier own setups.