Yeah, see a medical professional. Make sure it's not something other than the cycling. If you get a clean bill of health, consider shoes with even stiffer soles and playing around with cleat adjustment. I found that my feet feel best with the cleats slightly toward the outside of my foot instead of directly over the ball of the foot. But, see a medical professional first.
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A conclusion is the place where you got tired of thinking. - S. Wright
Favorite rides in the stable: Indy Fab CJ Ti - Colnago MXL - S-Works Roubaix - Habanero Team Issue - Jamis Eclipse carbon/831