One ugly hack is to get things configured as you want, then shutdown Kodi from the console and copy /storage/.kodi/userdata/guisettings.xml to a location like /storage/.config and then use the /storage/.config/autostart.sh script (which doesn't exist unless you create it) to copy them back to /storage/.kodi/userdata on each startup. This forces known-good settings to be used instead of the probably corrupted settings that weren't saved correctly on shutdown.
Thank you, I think that is what I will do. I don't ever change the settings once they are set so this will work fine.