Have you tried this? I'm not sure if you went to PT but this is one of the things that helps me. I had surgery on my knee in 2006 and couldn't walk after a 'simple' scope surgery to remove bone frags and trim my meniscus. To tell you the truth if I don't ride, my knee bothers me.

So back to the self myofascial release, it's basically giving yourself a massage with a foam roller. Roll your IT band, quads and calves and it takes a while but it helped me. I had fluid on my knee for the longest time as well and I did water therapy which is what triggered me to go into part time personal training but that's another story.

You can get the foam rollers through www.performbetter.com and I think they are about 3 feet long. You can also roll your back with them, which for me is HEAVENLY. Especially the a.m. after a long mtn bike ride.

Chondromalacia is usually what they say when they detect crepitus (popping and cracking)- kind of a blanket diagnosis. I would find a good sports med person or orthopod. But the orthopod usually wants to start cutting you open. I'm having the same kind of problem right now with a foot injury from Oct where I shoved my foot between two rocks when I was riding. I think alot of it is just getting it stretched out but it hurts like heck. Good luck!