I would adjust your stance for sure. How wide do you have your stance. If my stance is to wide, I have found that it bothered my knees. Also what angle do you have your bindings set? This could also be an issue. I don't think that it is your boots. Usually your feet will start hurting before your knees, but new footbeds might be a good idea. Play around with it until you are comfortable as possible. You should be able to find a happy medium where you can ride all day long and feel good doing it!!