We all have different body organization issues, and one person's physical therapy might not work for another person.
For example, as part of my therapy routine, I stand on a wedge with my toes UP and my heels DOWN; but maybe I misunderstood Punished.
People have different kinds of knee pain.
Some people have pain below the kneecap, some behind their kneecap, some to the left or right of their kneecap, and others have pain in the back of the joint or deep inside the joint.
Still others have pain that comes and goes, unpredictably.
All of these types of pain involve different types of body organization, and different types of repeated-use injuries.
Riding a fixed gear bicycle reveals knee issues.
It doesn't cause knee issues.
If anything, riding fixed will help heal knees, IF a person has a good fit with his or her bike.
The amount of bike culture myth regarding bicycle fit makes it difficult to acheive a good fit.
Basic rule: knee over pedal and knee slightly bent with heel dropped.