Try to do some excercises that strengthen your quads. I have had knee problems my whole life, and running has always been painful. However, I have noticed that if I conciously think about 'bracing for impact' when I run, I can run with little to no pain in my knees (only everywhere else!!!). This 'bracing' action has become much easier as my quads have gotten stronger, as they are the key muscles involved. Try doing 20 or 30 bodyweight squats whenever you can find time-they work wonders!