One way this problem manifests itself can be seen in Catalogs -> Products -> Association.
When a "patch" is made in classes/shop/Shop.php at getCategory() to forcibly return a "1" every time, a more desirable result occurs.
However, without the patch, the behaviour is that the category tree is rooted in one of our subcategories.
I simply can't work out why this is happening, because in the database table (ps_category), that 2nd category is neither defined as a root category nor does it have a id_parent of 0. Any help or insight into this will be appreciated