MiSTer-dev have admitted (after much user complaining) that calling something "auto" and not having it be 100% automatic is probably a bad thing. Problem is the MiSTer menu itself has no way of doing something until you bring the menu up. It's not like a service running in the background. But they should rename that "auto" feature to something more blatant, like "flush to disk on menu open" or whatever. Even then, I make sure before I power off my MiSTer to hit the "save to disk" button to be sure to be sure.