From time to time, we see situations where the in-course navigation isn't displayed. We don't see the Units, Notifications, Discussions links, etc. We're not sure why that is as we have all of the options that we can think of enabled.
We have a situation now where that is happening in one of our demo sites. Here is a screenshot:
To see this live, I have enabled support access to our site. It is in the demo.grapevine.education site and the course is Course Technology & Learning Design.