I came across the same issue in Moodle 2.4.5 and found the following. Within the navigation settings you can set the navigationlimit. The description is: ’Limits the number of courses shown to the user when they are either not logged in or are not enrolled in any courses.’
However, after a long investigation I found that this number limits courses and categories displayed in the navigation block when a user is logged in and enrolled in courses. Within lib/navigationlib.php function load_category:
$limit = 20;
if (!empty($CFG->navcourselimit)) {
$limit = (int)$CFG->navcourselimit;
}
To show all courses and categories within the Navigation block I set the navigationlimit to 100.
I also found if a user is enrolled in a course within a category-subcategory-subcategory, this will not be shown in the My Courses section of the navigation block. Does anyone know how I could fix this?