I had some chondromalacia about 15 years ago, and after 2 physiotherapists misdiagnosed it as patella tendonitis, the subsequent rest, stretching and icing for a month did nothing. A 3rd physiotherapist diagnosed chondromalacia, and
the pain was gone in about 4 days after doing straight-legged kicking exercises with light weights.
Only a few lbs was enough for me -- 10, absoloute max. In fact, I started off with a heavy boot with a 2.5lb plate taped to it.
The way my physiotherapist explained it to me is that during normal quad contraction (knee extension) the middle quads (both?) pull the knee cap up and out of the way of the end on the femur, but when fatigue, overuse, or imabalances develop (or whatever) the firing order of the quads stuffs up, and the rectus femoris doesn't pull the knee cap up quickly enough, therefore, causing the cap to grind on the femur and the subsequent pain. As far as I know, it's somewhat common for this to occur amongst cyclist, coz the middle quads don't get worked as hard as the mediali and laterali
The straight-leg exercise somewhat islolates the middle quads (rectus femoris and vastus intermedius) and corrects the tone imbalance. The leg doesn't have to be dead straight, just so long as the dominant movement is hip flexion, and not knee extension -- and try point the toe in such a way as to affect upper quads, and not the groin