I agree about getting insoles of some kind. I do a lot of hiking and backpacking and I have a bad habit of turning my left foot inward which causes a lot of pressure on my knee. I bought Superfeet insoles for my boots. They are kind of pricey but they help keep my foot in place in my boot and my knees comfortable. I should get them for all my shoes. As I sit here I can feel the pain in my knee from turning my foot in my dress flats just as I walk around the office.
Perhaps, like me you turn your foot strangely when you walk as well causing undue stress on other joints. You should watch how you walk and if you notice a turn of some kind maybe find some shoes that might help your gait.
In the mean time, take care of yourself and feel better