I had similar with 10.6.2 (I think) Built Stonehenge, didn't get borders. When coming back to the game the next day, 100 turns later, loading a save, voila, borders expanded!
Though in this same game, all puppets went to 1 pop, and no pop was working anything, so puppets were stuck frozen dead at 1 pop. So might be totally corrupted save due to unforeseen consequences. Maybe updated mod mid-game, not sure anymore.
Sorry that I can't be any more specific.