In the File|Folder Permissions table look at these 2 columns: Script Owner User ID (UID) and File Owner User ID. The numbers that you see in each of those columns should match. Or in other words, the numbers should be the same for every row in that table. If you see a table row with numbers that do not match then that is where the mismatch is occurring. Let me know what you see.
A few people have run into a problem with the DB backup folder having a different Script|File Owner User ID. The quickest way to fix this problem is to use the DB Backup > Create Backup Jobs Accordion Tab/button > Rename|Create|Reset Tool. The Rename|Create|Reset Tool renames the DB Backup folder, which corrects the Script|File Owner User ID problem. The root cause of the problem occurs when someone does a website move/migration/clone. I’ll automate a fix for this or add additional help info in the BPS Mismatch Notice.