I have/had the same problem. Use to run fine back in errr...1998? Anyway, I wanted to play this again because there have been no REAL Star Wars Space sim games. Even with all the new movies. Installed it last night on Win2k. Still fun, once you get the, autoexec.nt file in the right place, font fix, and run it in 1600x1200...unheard of back then : )
Here's my fix for this problem:
Copy the files from the cd /Movies directory to your install/Movies directory, assuming you have the disk space(this is 2006 after all). I've only done the first CD, Intro and Prologue. No stuttering. I assume it looks here before looking to the CD. Should work for CD2 as well, I'll do that when I get around to it.
Now, why can't someone make a new Xwing game, or a Clone Wars space sim game? C'mon, Xwing is just deep enough to be enthralling but accessible enough to NOT be Falcon 4.0+ in space.