If you enable Show my course categories (navshowmycoursecategories), all courses are populated into the nested categories, even ones the user isn't enrolled in.

In 3.1, the sidenav would look like this:

But in 3.2 it now looks like this. Notice the addition of a course the user isn't enrolled in:

While this may seem trivial, take a look at this from our production dataset test site:

I am enrolled in courses in that expanded category, but I can't get to them, because they are crowded out by non-enrolled courses.

It even includes categories I have no enrollment in (Summer 2016).