I have had these shoes for a year and have changed my clips twice thinking there was something wrong.  Turns out it was the shoe - it's wide!  My foot must be narrow but this shoe really hurt.  The last straw was yesterday when I moved my seat up and down thinking I was pushing too hard oh the pedals and that was causing the problem but they were still painful.  Anyway, back to REI they went and I ended up purchasing a pair of Giro's.  A lot more money but as long as they last a couple years and feel good, it will be so well worth it!