I just upgraded from 1.5.? to 1.7 and now courses are being skipped. They are hidden courses but some of them have changed since they are being developed.
Previously all courses were backed up no matter what - I don't have a large number of courses or very large courses so that was okay - I at least need hidden courses that have changed content to be backed up.
Strangely one hidden course which has no changed was backed up. It was recently created and the instructor hasn't logged on yet, yet its been backed up each time.