Mine do too! Considering how so many people here on the DIS rave about Keens, I thought I just had weird feet.
I've tried relacing them numerous times trying to make the fit better, but they just kill my feet. I made the mistake of wearing them shopping one time and came back with blisters/red spots on the balls of both feet, on the top of one foot, top of one big toe, and around both little toes. That was the last time I tried to wear them. For some reason my feet just don't like Keens. Mine are the Keen Newport and the guy at the sporting goods store recommended them and even tried them on me. I didn't think they were comfortable, but he assured me they were the right size and I just needed to break them in.lol I haven't worn them in the last two years.