I can't believe everyone said to visit a variety of medical professionals, try different pedals, saddles, etc. but I don't believe anyone has suggested simply seeing a different/better bike fitter? Not all bike fitters are created equal IMO.
I had your problem back in 2009, and had an appointment with a knee surgeon, because my initial pro-fit only helped a little. Then I paid Nate Loyal in Santa Monica 180 bucks (and felt like a complete tool for doing so) and my knee problem was gone AND I got much faster and cancelled the appointment with the surgeon. That 180 bucks was very likely 1/100th of what surgery would have cost.
Sorry if you have already seen a different fitter, but if you haven't done that... Good luck and keep us abreast!