Chondromalacia
In the opinion of the doctor who has examined you, the pain you are experiencing in your knee(s) is primarily and perhaps entirely related to softening of the cartilage on the back-side or joint-side of your knee cap(s).
The cause of this softening is often unknown, although direct blows to the knee cap, or a jump from a height in the past may start the process. Pain around or deep to the knee results, often when using stairs. Also, stiffness after sitting may be noted, especially with the knees bent as in a car or at a movie.
Your problem is worsened by a conscious or unconscious favoring of the leg involved with weakening of the strength of the thigh muscles of that leg. Treatment for this condition is to strengthen the muscles, at least to normal. This may not stop the cracking and creaking in the joint, but it will improve the knee and almost all cases eliminate the pain. Most important, this will help prevent worsening of the softening. The exercises described below should be performed twice daily at least, until the pain stops or so that it does not interfere with normal activity.
Isometric Quadriceps Exercises
(thigh muscles, in front)
Lock the knee in the completely straight position so that the muscles are tight. Then lift the leg against a fixed resistance (underside of a desk, heavy chair, bed, etc…) Hold for five seconds and then relax completely.
Do this exercise 5 times and increase by 5 repetitions until you note a slight ache in the thigh muscles. Then build up the number of repetitions until you are able to do 20. Stick with 20 but gradually increase force of tightening as muscle power returns. You may stop when pain with use stops.
Alternate these exercises, or do several of the first and follow with the second