This problem could be related to two things: improper running technique and improper shoes.
For running technique, have you ever looked into the Pose method? check out: www.posetech.com
And for shoes, I really wouldn't trust anyone from a running store. They usually prescribe shoes with large heels. My advice: go with a flat shoe - the flatter the better. if you are running correctly, you don't need any kind of super-shoe. The Pose site also lists some good running shoes.