Your knee looks fine. Your doctor and all diagnostics rule out any internal damage.  But your knee still doesn’t feel right during that run or after box jumps or cycling past that 10th mile.
What gives?  
Yes! Make sure a qualified PT or MD who loves knees performs a thorough evaluation of that joint.  But just as importantly, the clinician must assess “above” and “below”; e.g. the hip and knee.
Instability. Poor motion or motor control. Balance dysfunction. Chronic (and ignored) hip pain. A painful bunion! The knee, as a hinge joint, transmits forces from the hip to the ankle (or,  when the foot is grounded, from ankle to hip). Disrupt normal mechanics above or below, and the knee could suffer.
Insidious knee pain. Know your “above” and “below” rule. And make sure your Physical Therapist does, too.
 
Move. Heal. KNOW. Evolve.