Are you flat footed? I got what is called Ilio Tibial Band Syndrome because of that, the tendon becomes inflamed and pain can manifest all the way down the leg to just below the knee.
http://www.youcanbefit.com/itbs.html. The physio gave me some exercises and I got some shoes to compensate for over-pronation. Worked fine, now I'm running evey other day, for long periods with no pain.
Good luck, it would be awful to lost the ability to run.