Picking Shadows or Lightning (but curiously not River, Earth, or any other spirit I've yet tried) before starting the game, then using the tickboxes to enable or disable any expansions, throws Error in Script (SetupChecker - SetupChecker): Object reference not set to an instance of an object.
It also stops Finder and Downpour's panels vanishing when bot JE and F&F are unticked, but doesn't stop the "Requires Badlands" and "Requires Tokens" spirits from vanishing at their appropriate times.
That makes me think it's something to do with "Requires Isolate", but without a line number in the error, I haven't been able to track it down yet. I can look more into it later.