You don't need to specify any game with that compiler. But you have to use the v-1.00 switch. Perhaps Fred's would work.
I compiled scripts with only the contents of scripts.bif on my computer before the release of the pc version without problems. You can drop them in any directory along with nwnnsscomp.exe and this .bat file:
http://www.starwarsknights.com/forumdl/nsscomp.zip) . However, I believe that Fred's script compiler asks for some specific settings but I could be wrong as I never tried it without the PC version of Kotor2.
If I understand he's getting the same error from both compilers. I really don't know what is causing this :confused: