Hello sarabear and welcome to the Pain Forum:
I think what you're experiencing is called Runner's Knee (Patellofemoral Pain Syndrome)
The knee is a complex joint. It includes the articulation between the tibia and femur (leg and thigh) and the patella (knee cap) and femur. The most common knee problems in running relate to what is called the "patellofemoral complex". This consists of the quadriceps, knee cap and patellar tendon. What is now called patellofemoral pain syndrome (PFPS) has also been called runner's knee, anterior knee pain, or chondromalacia of the patella. For many years runner's knee was considered to be a direct result of chondromalacia of the patella. This essentially means a softening of the cartilage of the knee cap. The anatomical sources of pain in this area is now considered to be from the richly innervated subchondral bone (bone below the articular cartilage), infrapatellar fat pad, or the medial and lateral retinaculum of the joint.
“...certain mechanical conditions may predispose you to a mistracking knee cap. ”
Cartilage does not have the same blood supply that bone does. It relies on intermittent compression to squeeze out waste products and then allow nutrients to enter the cartilage from the synovial fluid of the joint. During running certain mechanical conditions may predispose you to a mistracking knee cap. Portions of the cartilage may then be under either too much or too little pressure and the appropriate intermittent compression that is needed for waste removal and nutrition supply may not be present. This may result in cartilage deterioration, which at the knee usually occurs on the medial aspect or inner part of the knee cap. All patello-femoral pain though may not be caused by this mechanism, although uneven stresses across the joint are believed to play an important role in the development of pain in this area.
I hope this was of some help to you. Please take care.
I also have patellofemoral pain, and it is a mean bugger. Lying down and lifting your legs up and doing phantom chairs will strengthen some of the muscles in your thigh. Also, you can try to push the kneecap towards the interior of your legs a bit. Realigning the kneecap helps with the "popping" feeling.