Turning things off won't change them, you'd have to remove the elements. I don't know if topo can be room bounding, but the odd shape of the bounding makes it more likely. It will be something at the rooms computation height (0' is the default) It could be a finish floor or a linked model with room bounding turned on. If the topo is inside the building modify it so it is not (usually done by adding a building pad). If topography is made using elements like floors or roofs they might contribute to it.

I'd start by cutting a section through the offending areas and seeing what's there.