So we've found a little bug that is quite frustrating. Some of our courses were not showing up in the front-end. It's as if there weren't there even though we could see them in the backend. This was on a course category template and the courses were assigned to the category.
What we ended up finding through some testing and trial and error is that until we 'drag and dropped' the course (or a course assigned to the same course-category) in the course list it wouldn't show up. As soon as we attempted to reposition the course even if we didn't actually change the order then the course would show up.
In the 'Course Order' setting we are using Post Order Number and ascending.