Hm, this is kind of a late response, but it reminded me of a problem I had a few years back so I thought I'd chime in. I was getting sore knees in a similar area to what you describe, and I eventually went to a physio. She said that a combination of a desk job and biking a lot were aggravating my tendency to be a bit sway-backed, and due to the way nerves and things are connected, the pressure on my lower vertebrae was causing my knees to hurt. So it wasn't actually a problem with my knees at all, but with my lower back.

She recommended lots of stretching of hip flexors and strengthening my lateral abdominal muscles, along with some other things like paying attention to my posture when seated and walking and doing exercises to loosen up my lower back. I took a pilates class as well. Seemed to work, my problems went away after I followed her advice.