Are you turning them off with keyboard shortcuts after they are automatically turned on for a tutorial? I’ve found that you need to go into the settings menu and turn them off there for the settings to be stored, otherwise they will come back on next time.
In that case, it might settle down after a while and remember the settings. As I recall from when I only used a controller, it would take a few days after an update or DLC download before it started remembering again. It’s been a persistent issue that hopefully DTG can fix.