Do you get any back pain at all? Any stiffness in your hips even if it's not painful just a bit tight?
I think my knee pain came from having a tight Psoas. A chiro helped teach me how to keep my lower back loose and that helped.
I find when my back is bad, knee misalignment and pain follows. No back pain, no knee pain.
I'm working on stretches that might help keep my hips loose now.
Here's a passive stretch which works wonders for my lower back and a website on the Psoas muscle just in case any of the symptoms ring true for you. This stretch is good but I'm also looking for more.
http://i155.photobucket.com/albums/s.../lowerback.jpg
OK the pic above is the closest I could find to it on the net (that's not me). Add a chair to support the legs, lay your arms open and straight out to the side and put a small pillow under your head if you want. Lay there for 15 mins and you'll feel AWESOME!
There's a pretty wide range of symptoms so check it out even if my symptoms sound different from yours:
The Psoas Muscle and Back Pain on Squidoo
Good luck :)