Hi,
The category_pathway indicates from where the custom came from.
Without this information, HikaShop have to find the first "place" where the product can be displayed.
Because you don't have the category_pathway, HikaShop have to find the first "place" where the product can be displayed and because you have a "list all sub elements", the product can be find in the first element.
It is a logical result but I understand your requirement, which require some specific development (which is not a little development, it has a lot of side effects).
This feature is already in our TODO list but I don't know when it will be implemented.
Regards,