So I've been playing in DC for awhile and finally decided to venture to the Mojave. I went to the train station as described and it seemed normal (unless Judiciary Square Metro is the right door to go into). It seemed that the rubble wasn't cleared as it was supposed to be, so I used tcl to see if it was behind it and I still can't find it. I'm running 2.4a (doublechecked on NVMM) and I'm using a clean install of the FO3, FNV, and TTW. I've never installed TTW prior.
Here's a screenshot of the local map inside the penn ave: http://i.imgur.com/8O9PlWr.png
Screenshot looking down at the tunnels on the east side from the raised platform between the mall and penn ave: http://i.imgur.com/GeRpkdW.png
Screenshot at the end of the the tunnel that has the door to Judiciary Square Metro after I used tcl to get through the debris: http://i.imgur.com/SjCh6lp.png
which is strange because other people seem to have the "rubble is not missing" problem but still have the door to go to the new station. It is like there is no station in Veritas game (or at least no door that leads to the station).