yea i get this too if the straps are too tight, especially the middle one, so i keep it loose.
i keep it loose enough that my heels slightly slip in my shoes when i'm walking. then its usually fine when i'm riding (don't forget, when you exercise your feet swell slightly).
another thing is, specialized do an insole with a padded "button" under the ball of the foot that works to keep blood flowing through the foot. i'm not sure how much difference it makes bcoz i've never worn anything else so can't compare sorry.