by Ken Task.
Logs may/may not say something specific ... sometimes a 'clue' though.
As I understand the backup process, if a course hasn't changed or if a course is hidden it's supposed to be skipped. There is a field in the tables related for date/time stamping - table mdl_backup_courses.
select * from `mdl_backup_courses`
The times you see are Unix epoch and one would need an epoch time translator to put them into humanly understandable dates. I mention this only cause I've seen some strange stuff occur when the system clock was off. Got server sync'd with a ntp server out there?
What if you create a new course. Pretty much blank. Then ran the autobackup .bat file?
Also, have you checked your moodledata/temp/backup folder?
'spirit of sharing', Ken