[quote=Greslin]
So if you upgraded from 2.2, it is possible that something went wrong during the update process. If nothing else works, build a clean 2.4a and move your mods. Do it right and your save games should be fine.
[/quote]
I manually uninstalled 2.2a, as per the instructions, before installing 2.4a. Thanks though. When I exited the new area it worked fine, I didn't have clip through the subway wall. I'm guessing it was from another mod or because I had been through the area before.