I'm having an issue with some courses not getting backed up, even if there have been recent changes. I came across this bug:
http://tracker.moodle.org/browse/MDL-25454
And this is exactly the behaviour I'm seeing. Despite recent changes, if the course is hidden, the backup is skipped. However, this bug is marked as resolved about a year ago. I'm using Moodle 2.3.2+ (Build: 20120927).
The documentation on automated backups doesn't mention behaviour being different in hidden classes. Despite the bug being fixed, I'm still seeing this effect. Is there some other setting I'm missing? Did the bug creep back in?