TTW adds edited FO3 masters to your FNV install, otherwise you wouldn't be able to play in DC through the TTW mod. If you're only seeing 2 other FO3 .esm files, then you need to be sure you have all the DLCs for FO3 and FNV...
Here's my .ESM load order:
If you don't have all the masters I listed, then you're missing things that you need for TTW to function...
“Ignorance is curable, stupid is forever.” - Robert A. Heinlein