So....really, you should see a doc if the pain keeps up after minor saddle adjustments and such. I could have pretty much written your post. My knees started getting messed up when I started walking strangely/adjusting my walking due to a neuroma (angry nerve) in the ball of my foot. From there, something happened, and basically my knee cap isn't tracking correctly, and has too much movement...so it slides around and hurts. I just started seeing a physical therapist for this. Apparently (based on her tests), I have really strong muscles in some places (the biking ones), and some major deficits in other places (hopefully stretches will be able to fix my problem). GOOD LUCK!