ahhh123,
You could be having problems with the ilitibial band (ITB), as it inserts onto the lateral aspect of the knee. The ITB is the continuation of the tensor fascia lata muscle. It can sometimes flip over the tibial condyle, as the knee goes through its range of motion. There is a bursa under the ITB there, which can become swollen and tender.
The fascial bands of the ITB become confluent with the ligaments which hold the patella in its groove. With you being pigeon toed, and with the ITB problems, the biomechanics of the patella in the femoral groove can become disrupted. This can cause popping, maltracking, and pain.
You can try stretching the ITB. By keeping the quads strong and the hamstrings stretched, the patellar tracking may be helped. If this takes care of the problem, great.
But, without a proper examination it is impossible to tell exactly what is going on. So, if this gets worse, you may end having to see an orthopedic surgeon. (I wouldn't waste my money seeing a general practioner, who will just tell you its an overuse syndrome, bursitis, tendonitis, etc but not be able to tell you where it is coming from or how to take care of it.
Good luck.