Ah, you have another controller attached; that can confuse the OS. Generally a game that supports only a single controller, as I assume the Vegastrike engine does, will look at ID1. I assume the Nostromo was probably on ID1.
I use comments when neccessary. There's not a lot of them there, but they do the job. Also, I keep my macro definitions pretty descriptive, too. For more complicated profiles I find it a must. The Privateer Remake profile compiles to 9% of the Cougar's memory. My most complicated profile compiles to 36%, and looks downright scary at times.
I have done the Uber-mod (v1), a long time ago. It probably wasn't worth it, as there is still center play. Someday I will get the Evenstrain mod done, or something even crazier, but IMO programability and customizability are even more important than physical precision in the Cougar, so I try not to worry about it too much.