Sounds like an ITB problem whih can cause patellofemoral symptoms - meaning your kneecap doesn't track properly when you run.

Some things to try: Use a tennis ball to massage your itb....along the outside of your thigh. You can try taping your kneecap when you run (I'd try a search on you tube for patellofemoral taping to see how to do this)
The other thing to look at is a strengthening programme.....one of the reasons your ITB causes problems is because it is tight, and it usually gets tight to compensate for weaknesses in other muscles. A good strength programme will sort this imbalance out.

Have a look at my website: Patellofemoral Syndrome (runner’s knee) Physiofixme

Hope this helps