This sounds like a classic case of runners knee.
Mine didn't change for about 8-10 weeks of constant re hab last year. Then in two weeks i went from not being able ti run 20 min in bad pain to being able to run every day.
Go to the physio and get some exersizes to do, and DO them everyday. make sure you work both legs though as I didn't and the pain intially transfered to my other knee!