I have experienced the same problem on my 98 Contour. When I first had the sheilds installed at the dealership, the car creaked and groaned while I was driving it out of the parking lot. They looked at it again, adjusted the shields, and handed the keys to me. Now the shields were rubbing the tires! Needless to say, I wasn't impressed with my local dealer. By the 3rd time they looked at it, they adjusted the shields and now strange noises. After a couple of days, the sounds returned. I will be complaining about it the next time I go back!
Is it just my imagination, or is the car a little harsh over bumps now?