Please take note, that auto-repair repairs an item to its 'original' state.
So, let's say you have a already Battered Shield, and then you turned on Auto-Repair, saved it, in-game if your Battered Shield turned into Unusable Shield, it will only repair it to Battered Shield instead of Normal Shield. Make sure you repair everything manually unless they're all in normal state, then you can turn on auto-repair again.