Are you closing kodi down properly using the second button at the bottom of the screen or are you just pressing the home button?
Not closing kodi properly causes files to get altered and build skin settings to be set back to standard
As for trying to stop your fire stick updating don't bother, amazon are highly unlikely to ever block kodi (with one of the updates it even checked for kodi and added it to the main menu if it found it)
They are fully aware that lots of there fire stick sales have come about from the fact people can install kodi so they are not going to block it, they did their part by removing it from their app store.