When I first started running I was getting pain behind my knees as well. My first question is--how long have you been running or are you just starting a running program? If you are just beginning a running program, it could be your hamstrings or your gastrocnemius muscle (the large calf muscle) that are causing you the pain behind the knee. Both of these muscle groups cross the knee joint. It may be a case of too much,too soon. When I developed this problem, I switched to a walk/run program and gradually increased my run time and this made all the difference in the world. Hope this helps.