If changing the movies so that they run off your hard drive does not work, then don't do it. Change it back, or reinstall the game to restore the old settings.
If you're having problems with a particular movie in the game, try and play it off the CD with Windows Media Player (open up My Computer, go to the CD drive, find the movies folder, and try and find which movie it is). If the movie does not play correctly, you probably have a damaged CD and should contact Eidos about getting a replacement.
[Edit] If you really, really want to run the game with the movies from the hard drive, but are unable to configure the registry correctly, you may want to try a virtual CD drive application like CloneCD's Virtual CloneDrive.