I have experienced this, and have second-guessed myself, but it seems to me that when using kotor tool as a compiler, I have to remember to change the specific output filetype to .ncs. I am convinced on my own part that those "failed" compilations are mostly user-error on my part.
I have never used nwnsscomp directly as my compiler, so I cannot speak to that experience.
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