Double check where the ball of your foot sits relative to the axel. It should be directly over it with the pedal at 9 o'clock. Slight adjustments can be made. I have high arches and suffered with a new pair of Specialised shoes with the Body Geometry inserts, tried normal inserts, higher Specialized inserts, then checked again, and the ball of my foot was slightly too far forward putting pressure on the 'ball' causing discomfort.
Best way is put shoe on and feel the ball of your foot and mark roughly the middle with chalk or some tape. Clip the shoe in and check the mark is roughly in the middle of the axel, if it's way off, that's your problem.