In the moodle navigation is an area for "my courses" where you normally see only the courses you are enroled in.

If you set navshowmycoursecategories in Site Administration --> Appearance --> Navigation to "off", you receive a flat list of your enroled courses (as expected).
If you set navshowmycoursecategories to "on", you receive ALL courses and ALL course categories of the system, however depending on the variable navcourselimit.

Replication steps:
This requires a site with multiple courses in more than one category. There should be a student enrolled in one or more of the courses, but not all.

1. Log in as a student in one browser.
2. Click on Navigation > Home > My courses
3. Note the courses shown
4. Log in as an admin in another browser
5. Navigate to Site Administration > Appearance > Navigation
6. Check "Show my course categories" (navshowmycoursecategories)
7. Save settings
8. Go to student browser
9. Refresh
10. Click on Navigation > Home > My courses

Expected result: only enrolled courses should be shown

Actual result: all courses and categories are shown