What pads are you using and how agressively are you using the brakes? Are you tracking the car? This information may help us understand what is happening. I don't think it is the spacers as that would create vibrations under all conditions and affect tire wear.
I seriously doubt you are warping the rotors but are in fact getting uneven brake pad transfer to the rotors. It behaves the same - really. Check out the technical articles at Stop Tech's website. BTW, IMO most service techs just treat the symptoms and not the cause, ie it's easier to replace parts.