The exemptions feature I can only imagine being a potential issue if you marked pretty much your whole database as exempt (e.g. you ran a very fuzzy search and chose "Mark all groups as exempt"). How many exemptions did you have? Without reviewing the code again I can imagine that to cause the logic a few headaches as it then tries to "reorganise" a large number of fuzzy groups.
Thanks for the feedback on the metadata variations - not had many people comment on that specifically as yet so glad to hear someone else is finding it useful.