I just thought of this this morning. It may be the way that you run. I assume that you run toe to heel like most of the world. I would honestly try teaching yourself to run toe to toe. When you run with those shoes that are supposed to be equivalent to running barefoot you are supposed to run toe to toe because there is no cushion on the heel. If you are really against this then maybe look into shoes with a bigger heel cushion, but I think the best route would be running toe to toe.