I recently found out I do this and that it's related to the knee pain/popping I have. I got some new shoes at a small, local store with real foot experts and the guy put little wedges under my inserts. I tried them for a week and although it felt weird it was also better. It's been three weeks now and I'm seeing real improvement.
I walk, don't run, so maybe you do need special shoes but if you can go to a similar place, it might help. (I wouldn't feel comfortable putting the wedges in myself because I suspect bad placement would be worse than none.