I was curious
From what I can tell in the code you turn on editing mode and then drag the courses into whatever order you want.
If that isn’t set then courses are sorted by the course sort order which is defined by moving courses around on the course management screen.
I'm wondering if there's something about courses being listed in the order activities were last updated, or possible the due dates for any activities in a course.
Anyway, the course overview block is being revamped quite significantly for v3.3. You can see a working example of the changes at http://prototype.moodle.net/myoverview/