I had this problem. I corrected it with a combination of:
-Stiffer-soled shoes. i found i had better power when pedaling, and my feet didnt get tired or cramped up because of the better support.
-Insoles, i also use the specialized footbeds. poor support makes feet very unhappy in several ways
-loosening the fastening of the shoes.. It doesn't need to be super tight in order to pedal efficiently. I have my shoes just tight enough to prevent my feet from pulling up out of them on the upstroke, and not much more. my comfort has increased considerably from doing just that.