You have just discovered what has irritated thousands of Lexus owners since 2007. The Nav system that only works right when the car stops. There is only one place that I know if that has figured out how to get around the lock out. Lexus will not help you with this.
http://www.prestigioussociety.com/testimonial.html
As for you rattle on the roof, its actually coming from under the car. The car design makes it seem like the noise is from the roof rack, but it is not. This cause is also well documented, just ask your service advisor about it. 15 minutes at the dealership and the noise will stop.
Good luck!
