After no results from rest, ice and stretching for a month,
I got rid of my chondromalacia in about 3 days by doing straight-legged kicking exercises with very light weights.
Weights aren't even necessary: I often taped a 2.5lb weight plate to an old, heavy boot, and used this.
A too low saddle position obviously is a contributing factor.
I'm no Dr Butt......
.......my physio explained to me that the pain is caused by the grinding on the knee cap on the end of the femur due to fatigue and a "slackening" of the firing order of the quads. Normally, during knee extension, the rectus femoris (or is it the vastus intermedius? one of the top quads) quickly pulls the knee cap up and out of the way of the femur, but when the quads are over worked, occasionally, the pulling up of the knee cap doesn't occur quickly enough.
In a way you're lucky that you were diagnosed with this. Apparently many people are incorrectly diagnosed as simply having patella tendonitis