When doing automated course backups, unless the course already has a row in the mdl_backup_courses table, the schedule_backup_cron inserts a row, but with a nextstarttime value of 0. This will cause it to fail on the following test:
if (!$skipped && $backup_course->nextstarttime > 0 && $backup_course->nextstarttime < $now)

Suggest that the new mdl_backup_courses row is inserted with a nextstarttime value of 1, or change the test to "nextstarttime >= 0 ..."