And also ensure you delete your …\My Documents\My Games\Freelancer folder completely, it probably has saved games from the mod in it…
After I learned what to do, I have never needed to play with the registry, nor fully uninstall the game - just deleted my \Freelancer game folder and the “My Games\Freelancer” folders and re-install from my CD and everything is always fine.
I also have a Virtual CD/DVD drive and converted my FL and other CDs to .iso files and use them by mounting in the Virtual CD/DVD drive.
I use Virtual Clone Drive, it’s free and superb:
http://www.slysoft.com/en/virtual-clonedrive.html