I had a widget that allowed me to hide or show pages – I removed that widget. I thought this might have been giving me the trouble.
After removing this widget, the menu was still was working as before. I did have a custom menu set up (in fact I had two).
I then deleted the two custom menus I had. At this point, the menu works correctly but every single page I have is showing in the menu bar. Not ideal either.
If I create a new custom menu at this point, it works as before with the navigation issue.