I have been having the same issue for weeks now, and finally got it behaving correctly again. I unfortunately did a few things all at the same time, so I'm not sure which one worked, but an accidental 'fix' is still a 'fix' right?
Here's what I did:
- Edit the navigation list by clicking Edit at the bottom of the Navigation menu.
- Open one of my misbehaving navigation items by clicking the 3 dots and 'Edit', changed nothing and hit OK.
- Turned ON the "Enable site navigation audience targeting" , Click Save.
- Immediately returned to the Edit menu and turned OFF the same button in step 3, Click Save.
I can't imagine why this last one would have had ANY impact , but maybe the 'read' trigger did something so including just in case:
- Opened the 'Site Contents' menu navigated to "Site Page" library and looked at the details of Home.aspx
At first it didn't work, but after refreshing a couple times, all my navigation menus started working again.
My GUESS is that there is a navigation script somewhere that bugged for some reason (mine stopped working with no apparent cause, I hadn't modified anything recently) and by resaving an item on the nav bar, and forcing it to re-write that bit of code for the navigation menu, it updated whatever header it was mad about.