I am using Moodle 2.5.
1. Under the Navigation settings:
a. Default home page for users/defaulthomepage is set to My Home
b. Show all courses/navshowallcourses is set to false.
2. Under the Front Page settting:
a. Front page items when logged in/frontpageloggedin - Enrolled Courses is the only item set.
3. Courses are set to manual enrollment.
Users are able to click on "Site Home" and then they have a link for "All courses".
Based on the setting I would expect that the "All courses" link would be hidden, preventing students from seeing the list of all courses in the system. They should only see those they are enrolled in.