I thought I had http://www.google.com/search?q=patella+femoral+syndrome

The BF assured me it was not. But, I did lots of research anyway. You might check your stroke. Are you using the full range, do your legs wobble (horizontal movement). Are you comfortable in your shoes? What is your cadence like? more hills?

strengthening is good. The basic ITBS pt exercises should take care of any stability muscles.

Me, I have pretty developed quads :-/ and it turned out I just needed The Stick as my muscles were messing up my tendons down there... My pain was bilateral and I, too, had pain going down stairs. It was more just below the knee cap.