All of the GNUstep files are there because if I set up the link from the oolite-deps/GNUstep to /usr/GNUstep then it works absoluetly fine even on machines that have never had GNUstep installed.It's probably not environment - it's probably a missing (and almost certainly empty) directory
I've adjusted the install script to check for the existence of a /usr/GNUstep and if not to make the link and I've got 2 other people playing around with it now. I'm sure we'll suss something out

My SDL_timer issue was unlucky coincidence and the framerate drop had nothing to do with the changes (and more to do with me being a retard). I also now know that the timer code I have to change is NSTimer.m and NSTimer.h in the GNUstep source. I really don't know a single bit of objc so this is something I'm gonna have to spend some time on, I'm thinking maybe next week.
I had my first chance to actually play today and I have to say that all you chaps have done an excellent job. I'm very impressed with the AI too, I'm pretty sure I saw pirates and police stop wailing on each other and engage a thargoid together... I almost wet myself with joy

I've got a few other unixey boxes kicking round that I'm going try and build some self contained packages for... FreeBSD 5.x, Solaris 10, NetBSD 3.0. Hopefully GNUstep will be a little more co-operative on those platforms.

Thanks winston for all you help, it's greatly appreciated. I can provide the bodgy IRIX standalone if you'd like, unless you would rather wait until I get it completely sorted?