Make sure your crankarms aren't too long for you and that your cleats are perfectly aligned (even if they have tons of float). Has your PT analyzed your pedal stroke, and/or has your fitter measured your knees' flexion at the top of your stroke? What about your walking/running gait?

Years and years ago when I still had 170 mm cranks, stretching before a ride would normally keep my PFD from flaring up. I'd just kneel barefoot, *ss on my heels, for 2-3 minutes.

If your PT isn't working with your feet, if I were you I'd at least raise the subject - foot strengthening exercises, orthotics, something as simple as a pad under the first metatarsals if you have Morton's foot (which depending on whom you ask might be pretty common)?