HI,
I was reviewing an article about a distance rider in a local paper, and he had problems with his knees and they became worse when he road until the bike was set-up correctly for his use. Seat height ,
Angles of seat, knee flexure to use or not use clips. even the crank lenght can effect the knee. so be sure it not getting worse from allignment issues on the bike.
My left knee pops if my seat isn't all the way back, now my legs feel like springs when the pedal bottoms out instead of knee pain I feel power...
Doug