I agree that chondromalasia is a reflection of a problem, but at this point it sounds advanced, so the game plan is different. What it sounds like is a force production problem, a technique issue where you are doing too little hip extension to turn the cranks and therefore using too much knee extension.

This is the most common error I see. The solution is to improve the coordination in glut max so you can better turn the pedals from the hips, less withthe knees. Easier said than done. What is interesting is that most people with this problem have an easier time when grinding, I think because it is easier to push from the gluts when your legs are moving slower. The problem there is as everyone will tell you, it shreds your knees after a while.

The best solution is as I said, try exercises that improve your ability to fire your gluts first, as you improve your control you'll feel an improved ability to use them on the bike. Try this exercise first http://cyclingphysio.com/?p=132

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