The problem for some people is that their shoes are lower in the center of the toe-area footbed than they are on the edges. This causes a pinched nerve in that area. Shimano footbeds come with a built-in metatarsal pad which is said to correct this problem. In your shoes, you can try to build up the center of the footbed slightly with strips of adhesive tape. Doesn't take much. There are also metatarsal pads available like Dr. Scholl's.