Hi Canadian-Ice,
I've had Chondromalacia / Patello Femoral Syndrome, not sure if that's the norm but in my case it's about the knee cap moving too much laterally when bending the knee (because the groove is too shallow), therefore rubbing against the bone cartilage and producing inflammation and pain.
For me it started in my teens, and it went on and off for quite a few years, and examined by quite a few doctors / physios as well. Nothing seemed to fix it.
As Hernanu explains, an adequate exercise program to stabilize the knee (both in terms of strength and resolve the muscular inbalance) will help to "fix" the knee more in place.
It's crucial to stop first the activities that exacerbate or produce the symptoms, then gain that strength and muscular balance gradually. For me one of the keys was that the leg strengthening exercises (mainly leg curls and leg extensions with weights) must be done with LOW angles.
The reason is, if you bend the knee more than 30-45 degrees under strain, the knee cap will be displaced and you're rubbing at the same time you gain strength, and it won't work.
I did leg curls at no more than 90 degrees, and leg extensions at 30-45 degrees. Eventually, once you gain lots of strength, you can do squats or leg press, but up to 45 degrees or so.
I couldn't run for years for this reason. Eventually, I have done 2 marathons (until the hip stopped me!).
Good luck, let us know how it goes...