So several people here have mentioned tracking problems and these are the core issue with chondromalacia patella. Other peeps have touched on the orthotic thing, I agree with the above. VMO strength is important but so is flexibility. All my CP pts get an eval for overall muscle flexibilty in the lower extremity. Typically they end up stretching the following muscle groups:

Tensor fascia lata (TFL)
Hip flexors
Piriformis
Calves (both the gastroc and soleus)

Sometimes:

Glute max and hamstrings

Apart from VMO, you may need to strengthen:

Hip adductors
Hip external rotators
Deep abdomenal/core muscles and pelvic floor

Manual therapy can be helpfu:

Muscle stripping of the Vastus Lateralis (this hurts like he!! but works)
Pelvis balancing
Assisted stretching of TFL and hip flexors

And if that doesn't work:

You may need have someone look at your back and do a manipulation of the pelvis and or lumbar spine.

Patellar alignment is about the whole lower extremity and not just the knee. Most often conservative treatment falls short because issues at the hip are not addressed. The nice thing about treating the hip is that it helps and you don't have to go anywhere near that nasty swollen knee.