thanks for the reply tdford. Does your brake pedal move about 1" up to the fully upright position when this sound happens on your vehicle as well?

 

While the clunk definitely moves the pedal and causes it to actually give a small clunk, it never sits low before the self-check. If it is actually dropping down on its own before you start it up and then coming up with the self-check, you may have a problem. Take it to the dealer... at least it will be documented if there is a problem with brakes in the future. You've got a 5 year warranty. Use it.