Not sure. The ITB could be something to do with it. A tight ITB could be stressing the patelo femoral joint when you work the quads while the knee is flexed as in the activities you have described. There are related bursae (cushions of synovial fluid that reduce of friction of tendons sliding against bone and other tissues) that could be inflammed.

Has your physio observed you performing squats, lunges and stair climbing? Your physio should work with you including doing weights to work out the problem.