I've got a few more questions for you:
1. Is your current Gold version from Steam? Amazon?
2. Where do you have the game installed - the path to it, ie: "C:\Program Files (x86) \Ubisoft" or some other?
3. Are you attempting to use Manual-Targeting? Have you tried Auto-Targeting? Does that work correctly?
Post back with at least that information please. I am guessing that you used Ubisoft's
Official v1.4 patch on top of your original DVD-R disk, correct? If so, GFO will not work correctly on top of that, only the Gold Edition that you have. For mods to apply properly, you must not have the game installed in a Windows "protected" folder, such as on of the "Program Files" folders. Windows will un-do most parts of a mod when the game is installed there. If you have a disk version of the game, you can just copy the game's folder contents and paste that into another folder of your own choosing, but if you have Steam or a few other download versions, then it gets more complicated, but can be done. If you do not have a lot of games, it is most likely easier to reinstall the game in a different folder of your own naming. You should also delete the Save folder to clear old data when you change mod configurations.
If you do have Steam, you could read
Moving a Steam Installation and Games for more information...