Thanks for responding, Ben. Unfortunately that does not solve the problem.
"permissions explicitly set from within each course", I am referring to going into the course and enrolling individual users. We have a number of user who have system roles, usually as a course manager. We would like for all courses to show up in their course list when they log in, since they are responsible for managing certain aspects of these courses. Since we have disabled the "all courses" list for security reason, these users are not able to get to the courses unless they know the "course id" and put it into the url string.