It sounded like patella problems. A sunrise view is the only stay that shows this. There are so many factors that control or contribute to the patella and none of them are conclusive in the literature.

The most common association seen in most study's is weak hip external rotators.
The VMO is a very tiny muscle, relatively speaking, and can not be activated preferentially over the outside vastus lateralis. There is a tiny patellofemoral ligament that is the primary restraint from the inside, or medial aspect of the knee.
If patella tracking is the problem then the therapist should be able to immediately change it by taping or using the appropriate brace then having you do what normally hurts and it shouldn't with the change the therapist ads. If that is the problem it is easily diagnosed that way and gives the way to start treating it.