@stenoflacon. Ok, it is really hard to help you when i can’t experience what is going on. I appreciate your explanation, but I don’t really understand what is actually going on. As long as there are files in those subfolders, clicking the subfolders will expand. I know this not only because I made the plugin, but I use it on my own sites for this purpose, and I just retested it on my local servers.
I don’t know what you mean by “merged the two articles together and I can now expand the folders from the second article”. You don’t need to have 2 listings in the same article, although you can by using offset parameter in the shortcode.
As long as the subfolders contain either files or other subfolders, it will expand. If there is nothing in the subfolders, there is nothing to expand, unless you allow the empty message to show. Here is a screenshot of the tests I did.