my 2 cents

cycling is alot of hip flexion, his ITB/TFL might be over dominatant and flexing his hip and causing knee pain have you checked his inner range psoas ( seated ant tilt and passive hip flexion then get patient to actively hold while you resist to nuetral) if psoas is weak then he might be getting a hip impingement problem. You also might have to corect his movement pattern if its faulty, you can strengthen all you want but if he isn't using the correct pattern then impaiment can set in.

I would recommend having a read of Shirley Sahrmanns' book on hip impingement. please tell us how your patient gets on

cheers