Over 5 years editting mods and I did not know you could place scripts out of the .iwd files...

Anyway, I can't install libcod cause the server is rented.
About the pure server issue - whenever I changed a .iwd file, people downloaded the new file and got kicked because of the old one (if it wasn't deleted). But, like I said, now I know I don't need to modify the .iwd.

Looks like the best solution for me is to take the scripts off, very simple.