It doesn't throw an error at all, and it zips is a handful of user image files, a few forum files (and many folders), a couple of course files and a small moodle.xml file... But it is not near a full backup.
I think maybe it may be because the id of the whole moodle site is 428 (i.e. there 427 courses with id number less than it and it and only 20 are after it). What effect do you think this will be having to backups and if you think it is the problem what is the best way to resolve it?
Another possible casue of the problem is that I do have another mysql cron job in operation that backs up my mysql database. Do you think this may be interfering even though they are set to run at completely different times?