Types of Knee Injuries
Check with your Doctor and ask Good Questions!

Runner's Knee: The first symptom is usually stiffness, especially after sitting for a long time.  There's pain inside and around the knee_a general ache.  This condition can occur when the (floppy) foot rolls in and puts great pressure on the inside and the middle of the knee.  The leg rotates and the patella often moves outside its normal path, wearing out the cartilage.  As time passes, this may become chondromalacia-a true medical problem where the cartilage softens and begins to disintegrate.  Early chondromalacia is felt as a "creaky" joint, with a rough feeling under the knee cap.
Tendonitis:  This is pain on the inside or outside of the knee.  Tendons connect muscles to bones and they can become inflamed from a direct injury or overuse.  Floppy feet tend to get tendonitis on the inside, rigid feet on the outside.  

Patella Tendonitis: This pain and inflammation in the soft tissue just below the knee cap, or where it connects to the tibia, just below.  When I lived in Missouri, I was diagnosed with tendonitis. It's like have temporary arthritis and the pain can be very painful.  I am not sure if this is true but once I moved to California, I never had the pain again.  I am not suggesting that you move but ask your doctor if the environment could have something to do with it.
Plica syndrome is another, but rarer problem of pronators.  It involves a pinching and folding of the membrane at the knee joint.  Symptoms are similar to chondromalacia with pain around the joint line, either medially or laterally, but not always under the knee cap.  There may be a clicking sensation, which indicates damage to the meniscus, a shock-absorbing structure inside the joint.  
"Galloway's Book on Running"

This is information provided to you, the athlete.  Please do NOT diagnose yourself.  Check with your local doctor or physical therapist.  Each person is different and you want to make sure that your diagnoses fits your needs.
Happy and Safe Running!