Favorites in ES not saving on shutdown

I just completed setting up a new 10inch Picade and finally got the controls working correctly (originally had an issue where select would start recording video, not an uncommon problem it seems). However I have now noticed a new problem. When I press the power button to shutdown the script closes ES and starts a shutdown of the Pi, which does seem to be working as expected but none of my favorites or other changes that I made in ES are being saved. Is the shutdown script actually properly shutting down ES to allow these changes to be saved?