I have two problems at the moment. They both seem familiar to me but a search turned up nothing on both.
First, my New Vegas story does not start after taking the train there from DC. I flip the train switch, Nine Years Later splash appears, New Vegas intro plays, and I appear in bed in Doc Mitchell's house with him staring at me. Nothing further happens.
Second, the New Vegas super mutants have both the FO3 and FNV textures overlapping simultaneously. The FO3 super mutants appear to be fine.
I reinstalled TTW not long ago to try and fix the New Vegas start, but the problem survives. Help on either or both would be lovely.
Windows 7, i5, 16GB RAM
Fallout 3 GOTY Steam
Using NV Anti-Crash, NV Stutter Remover, Sheso's Memory Thing,
Nexus Mod Manager 0.49.1 (Not sure why it says .1 since I installed .7 a few days ago)
I removed the Install Info since it was irrelevant to what's going on at the moment. I reinstalled TTW via NMM.
Attached screenshots of the overlapping textures and Doc Mitchell's everlasting stare.

. I tested it quickly and I didn't see anything that could have conflict, unless of course you used it, pick to start in vault 101 and then take the train to NV and forgot that it was still active
since it is just a mod to choose where to start, my advice is to not enable it if you want to start the Fallout 3 side of TTW and if you have it enabled, then disable after you start the game because I guess it will cause problems based on what you just told us
.