Echoing ma6cb's issue...
I am using an RPi3 setup.
First, Thanks so much for all the work done by the osmc team to fork kodi for the RPi. I have always been a longtime kodi user and the osmc dork is all i user on my Pi, which is now my primary mediacenter.
I recently updated to the beta/rc V17 and everything seemed ok after I deleted the addons26.db and addons20.db to get past the initial sadface bootloop.
Since doing so I have had my hidden menu items (radio, tv, etc) reappear as if they were never hidden in skin settings and I have had the Video Calibration settings reset to remove my overscan adjustments.
I changed everything back then downloaded the two settings files, guisettings and the skin settings file. The changes did in fact save to those files.
I have fixed it multiple times, changing between skins in order to "work around" as ma6cb linked to did not seem to work.
It does not do it every time. Does not seem to necessarily follow a rhyme or reason. I do have my Pi plugged into a master/slave surge protector scenario so it turns on when my tv turns on and removes power when the tv turns off. I do always properly shut it down first, giving ample time for power down before powering off the tv (effectively unplugging the Pi).
If it happens again (reset of settings) I'll upload the logs created directly after.