You are getting too good at this, Craig. Your diagnosis was spot on.
The installer will delete all of the *.mcc files in every profile directory. This, in the event a LUA version changed, would cause the *.mcc files to be rebuilt. But after you installed, you copied your old *.mcc files, which basically defeated the installer's delete. So I think you just figured out why "sometimes" it appeared the installer didn't work.
Steve