How old are your running shoes? For that type of wear and tear you should get new shoes every 6-8 months. It sucks because shoes are so expensive, but if the supplements don't work, you might want to try a new pair. To me it seems like everytime I get shoes worn in the right was I start getting shin splints and knee pain signaling it's time for a new pair.
You might always want to check out a Track Shack or Fleet Feet, or other type of running store for a shoe fitting. They will video tape your legs and feet while you run in your current shoes and tell you the best type of shoes for your gait and stance. The diagnostic is free and you don't have to buy the shoes from them, they are usually a little more expensive than say Foot Locker or Khols.