Just wondering if your over weight and be getting extra stress on the knee(s) from just a normal every day life. Or how deep you may be squatting. For BB'ing, breaking a little lower that the 90 degree mark is not always required. Are you keeping the knee area warm, like applying a heating lotion, wraps, etc around the knees before doing exercises. Very important.
Might check the shoes you are wearing. Also the foot stance. Some find less stress (you would think it would be the opposite) with raised heels. Like on a 2" board/BB plates. Olympic lifters, who handle huge weight in the front squat, use built up heels in their shoes/boots. If doing leg presses pain free, than something may be wrong with your squatting form, the way the bar is placed on the shoulders or stance. If pain when doing leg presses, that might suggest a developing knee problem beginning. Loose or potential floating knee cap (probably not), tendon/ligament, nerve inflamed, etc. Or maybe something as simple as not doing enough light warm-up movements for the legs and keeping them warn during workouts.
A Cat scan is the last thing most doctors will offer you. Big bucks for the insurance people. Might consider not doing squats and select other leg movements. Or until you can figure out what's up with the left knee. Good Luck
Side Bar: I have been doing 50 to 100 Hindu Squats (bwt) before any leg work, even DL's. Seems to set up the legs and get the blood flowing very well. Keeping the area primed and warm.
