^^^ Did you use the vanilla .2da from your vanilla game files, by extracting the .2da you want to merge from 2da.bif?
This is essential... If you did this step, then I am not sure what your issue might be, although I would suspect that you are running Vista or Win7 OS... Could be a rights/privileges thing, make sure that when doing anything KoTOR related on a Vista/7 rig, that you do the same steps for modding things that you did to properly install your game.
Want to play a game of ME3MP?
Qui-Gon_Glenn on the software of which we shall not name.... add me and the enemy shall fall in chunks of crimson salsa