Have you tried unsubing and re-subbing? I've been trying to find bugs so this is the only mod I have on. Also, are you sure you mean the Lousiville Auto Shop? From your comment you sais you were clipping between the hall and stairs but the stair in the auto shop are in a storage room that you have to go outside to get to. If you are in the scrap yard the hallway between the two basements is connected but there is a little trick to it.

Seems to work! Good ol' Occam's Razor

the old version of the mod tried to detect if the various tiles existed and then apply changes to them. In the latest version I found a new way using mapping tools that should be much more reliable and I hope this will solve issues for folks who were experiencing these sorts of problems