What kind of shoes are you wearing? Most cycling shoes that I know of (and pretty much all of the ones that I have owned) have zero heel-to-toe drop, which means that they are essentially flat-soled shoes. If you are wearing shoes with a significant heel-to-toe drop, it may be putting your feet in an uncomfortable position on the pedals, which is exacerbated by time and distance. I wear Chuck Taylors while riding my crosscheck, and I have never had a problem.