Sorry for such a late reply Daniel. The 6500+ courses relates to course instances in Moodle. That is due to what we call 'unit standards' in New Zealand. In essence, they're modules that collectively comprise a course or programme. The other cause of the apparent discrepancy is that our Moodle install has separate course 'occurrances' for the same course - being a self-paced distance learning provider we often have multiple separate instances of a course running concurrently.
I hope this helps and once again sorry for the late reply, I stopped tracking the thread.