@j_hoppe. Thanks for posting.
To be honest, I don’t understand what problem you are actually having. You will need to explain or show what you did and what options you selected. Normally, I would ask for a temporary admin login so I could login and examine what you did and see the result for myself. I really can’t diagnose your situation based on what you have written so far.
For example, there are 3 ways to display a listing with AFL: Unordered List, Table, and Paginated Table. You may also setup the listing either through a menu item or through the plugin in an article. You have yet to explain which options you chose to use. If you chose Paginated tables, no subfolders will show. If you chose Unordered List or Table, the subfolders will show only if you have the “Show Subfolders” option set to “Yes”. In addition, you never provided a screenshot of your listing settings or showed what you entered for Listing Path. These are all crucial data that I would need to be able to assist you effectively.
in addition, please make sure to clean the sync before syncing again.