They are caused by bad preperation, shoes have Little to do with it.Marathon runners who run without shoes dont have bad knees, runners that do have.At a guess you started running 6 st overweight, so metasarbles arnt working properly so neither is your knee .Your hamstrings have tightened up because of bad gait.Stretch your Hamstrings and the whole leg properly take 30 mins doing it.You will feel the difference