Ah okay I didn’t realise the section itself was still there. Can’t imagine what would cause that behaviour, sounds like some obscure bug in the details panel code.
You could try using the Widget Reflector (Window | Developer Tools) to see if the check boxes are there but just not visible, but to be honest I don’t see where it’s going to get you. As I said, trying to debug the detail panel code when there’s no customization would be a nightmare. Sounds like it’s hacky workaround time to me!