I had the logic backwards. It should be fixed now.
Whatever you have your settings file set to is the default when you open the fuzzy panel. You can toggle between hidden and not hidden during your session but when you have completed your action(s) and closed the panel, it is done. Next time you open a panel, it will use the default.
I am not sure what your other issues are…are you still having them now, if so, please explain because I don’t think I understand.