Ok, do this: Take the transparent tile in the top left. Go on to the third layer, and run over every impassable terrain with that tile.
I think that before you merged the two, you erased everything on that side with a transparent tile that was not the one in the top left. Since passability is inherited from the tile on the top layer, it became passable. But I just tried it, and it works.
Basically, Falcon was correct. It's an invisible, passable tile on the third layer.