Hi Gustavo,
Thanks for your research. The backup instances feature is designed to work with the original creator of an instance. The database table jobflow_instance has a column created_by_id that stores the original creator of an instance and remains unchanged even if you change the owner of the instance to a different user.
So, if user A created an instance INST_1 and changes ownership to user B, created_by_id field will still contain A.
In your case, you are running backup instances as user B and that's why those instances are ignored. All that you need to do is to run backup instances as user A - the original creator of those instances.
So, it is running as intended and is designed this way to avoid duplicate instance backups - once when run as user A and then again as user B.
Hope this helps!
Partha