"For both I get 24 lines and the Start time is almost the same, in some lines time is different in 1 minutes, but mostly it's the same Start time."
Think about that ... same start time?
"Also there is 12 directories with dates Aug 17 & Aug 23. Inside these directories there is xml files, and other folders like sections,course,files,activities."
Where there any backup.mbz files in those directories?
If so how large were they?
If there wasn't a backup.mbz nor a moodle_backup.xml then that course backup failed for some reason. View moodle_backup..xml file to see course name then go visit that course to see what's in it. Those can be manually erased without consequence.
"Semester is not even started so there is not much action in the Moodle system right now, so I highly doubt about teachers taking backups, uploading tons of files, etc."
Seems to me that would be a very good time for teachers to be active in their courses ... including making a backup. But ... only you would know that about your own site ... if you'd been monitoring and have some historical info.
That would also mean that courses haven't changed .. right? Why would you need another backup of that course if it hadn't changed?
Is the finish time consistent?
Believe you said your cron set to run every 60 minutes? Think the recommendation is to run it once every minute now. Everything that cron does won't be executed at each run ... task list.
You might also consider increasing those time outs ... slightly higher.
'SoS', Ken