An orthopedist diagnosed chondromalacia grade II in late 2005. I had been away from the sport for 10 years and came back to quickly after all that time off and putting on about 30 pounds.
I had many of the same symptoms: my knee became extremely painful after prolonged periods of sitting down, rest didn't seem to help that much once the condition developed, and walking down stairs became painful. Curiously, the knee never hurts when I run. Anyone else find this to be true?
I have taken a multiprong approach, mostly because there are a number of reasons why a person may develop patellar pain.
First, I got orthotics. While they aren't for everyone, they were for me. I had numerous other problems, including plantar fasciitis, hamstring strains, and achilles' problems. I exhausted all options before the orthotics, but none worked. I simply pronate way too much on my right side, and minimalist shoes didn't help and neither did severe motion control shoes with super feet. With the orthotics, all my other problems went away, and they have helped some with the knee.
Second, I went to work on strengthening my VMO. Not everyone agrees, but most studies conclude that strengthening this muscle gives some relief of patellar pain (because the VMO can keep the patella from tracking laterally outside of the femoral groove, which leads to the friction on the cartilage). That has been my experience. People often recommend straight leg raises and isometric flexing of the quads. These help, and I do them, but I find other exercises are better. One is to do quad extensions with the bad leg, but only for the last 20 degrees of the extension. Doing the full range puts too much pressure on the patella. But those last 20 degrees really works that VMO. I also do wall squats, again only for the final 20-30 degrees. I don't flex to 90 degrees. It's somewhat hard to balance, but I try to do these with one leg in front of a mirror and really make sure my knee is aligned properly on these.
Third, glucosamine-chondroitin. Again, I think the studies are inconclusive on this, but I figured what the hell.
Fourth, stretching the IT band, strenghthening the hip abduction muscles, and hip flexors. Some say that a tight IT band pulls the knee laterally getting it off track, so stretching and strengthening these areas may also help.
Fifth, for whatever reason, hiking helps my chondro. I'm not sure why, but it does, so I try to hike every so often just for a change of pace and the relief it provides.
I'm now running again, about 20-25 miles a week, getting back into it again. It's not a lot of mileage, but I was away from the sport for many years, and this is more mileage than I was able to do before the orthotics and strengthening exercises.
Good luck to you both.