as with anything muscle strength imbalance/flexibility is the root of most pain. the minuscules is a problem, and it should feel more like a grinding pain than anything else. From what I've read, you need to dramatically increase your sulfur intake, MSM or Glucosamine-Chondroitin Sulfate is another great choice, but also onions & garlic or anything in the onion family will also be effective. The body can repair a lot of the tissue damage, but it needs sulfur and blood flow without increasing trauma to the site. so your high to ultra high reps with low weight is always encouraged from a physical therapy standpoint.
Flexibility doesn't always mean that you don't have muscle imbalances. Stretching is good, but if you only focus on certain movements, that may neglect hamstring, vastus medius, or glute development may cause the patella to always be pulled more heavily in one direction versus the others.
One last thing that is important to discuss, is scar tissue in the actual ligaments, if you have access to them (obviously not the acl/pcl) you can do some deep tissue massages to break up any scar tissue, this tissue can swell more than it should and rub against things it shouldnt and cause pain. Sometimes a little regular therapy can make you feel a lot better.
Good lifting, hope this helps a little