Ah... Freespace; what an awesome game that was. What you might need to do is check the video card compatibility. It might need to be run in a different resolution, as well. Right-click the executable file and click Propterites; go to the Compatibility tab. See if there are any boxes which state that if checked, to run the executable file in a lower resolution. I know that worked for Myst, but who knows with Freespace.
 
Also, have you checked the developer's site? They sometimes are pretty good about describing how to run old games on newer platforms. Seeing as Freespace was just plain amazing, they're bound to have some information.
 
P.S. Appropriate user name for this question. I likes