Hi poster! Pain which limits your activities of daily living is always a frustrating occurence. In the case of pain behind the patellae (known as retropatellar pain), there are a few conditions which spring to mind. The fact that the pain arises after running leads me to suspect that the most likely cause is a condition called 'patellofemoral pain syndrome' (PFPS). This is commonly caused, as you mentioned, by an imbalance in muscle contraction during straightening of the knee. The part of your quad muscle on the inside (your vastus medialis obliquus or VMO) is prone to firing too late, or being too weak to counter the early, strong contraction of the head of the quad on the outside (vastus lateralus or VL); this results in the patella being pulled through its track on the wrong angle.
In order to check if this is the case, try doing body weight squats, but stand with your feet at shoulder width, and toes pointing about 20 degrees out, rather than straight ahead. This exercise is more about muscle coordination than strength, so don't add weight, just go for repetitions, morning and night (doing it while brushing your teeth is a good prompt). Really concentrate on contracting the muscle on the inside of the thigh. After doing this for 2 weeks, go for a light run, and see if there's any improvement. If so, seeing a chiropractor, osteopath, or physiotherapist to release the VMO, and tape for the knee pain, as well as assess the cartilage behind the knee cap to see just how much damage has been done is a great idea.
If there has been no improvement, it is still a great idea to visit one of these specialists, as the amount of time you have been suffering (chronicity) means there may be some damage to the joint surfaces.
If you are in the metro or Fremantle area of Western Australia, I'd be happy to examine the case, as I work in a gym, providing treatment to a number of professional athletes, and have a direct referral relationship w a knee specialist should there be any more concerning findings.
Let me know how things progress over the next two weeks, I'd be interested in any changes.
All the best,
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