I just made a new tileset on a blank project and set some quick impassable tiles. Unsurprisingly, it worked.
Import those same tilesets onto a blank new project and set some impassable tiles. Check if it works.
If that's the case, then indeed something else is interfering... I can only imagine a script... Do you have any script in your Database that does anything to Tilesets? I really can't grasp at anything else, sorry.
In the meantime, I gotta go to bed, so good luck and be patient with this. As I said before, try these tilesets on a blank project and see if they work. If that's the case, then try and find a thing that's causing those custom tilesets in your main project to be all-walkable.