I have patellofemoral pain in my right knee... I did physical therapy for it for a couple months in 2001? I haven't kept up my exercises like I should, so certain things do flare my knee up.... skiing, going down hill hiking, etc.

For the most part cycling doesn't flare up my patellofemoral knee, provided that I have my seat at the right height, I use 165mm cranks, and I use speedplay frog cleats.

Has your physical therapist taught you how to tape your knee cap in place and counterbalance your improper tracking? That worked really well for me when I was having constant patellofemoral pain.