BAH! I got it. Under your games/Fallout/user/saves file, if you have a saved game already stored there, you need to change THAT falloutprefs.ini. I had been altering the default prefs, but when it logs you into LIVE, it loads your login pref.
Can these colors be used for both the user interface and VATS? Ive done everything I can imagine to get this to work, and still no luck. Just out of curiosity, does changing the color in options after you've loaded with the new color invalidate the change?