In reply to toasted:
For me it's a friction thing. Part of my thought is the stiffer soles make the foot slide about more as they don't give/flex as the foot is used to and this causes excessive friction between the foot and the insole.
If your not used to stiffer soles, then your feet may have to get used to them? Are your feet moving a lot inside?
I've had the ball of the foot affected with new stiffer footwear in the past and this has always cleared up when I built up the use of them slowly. When it's happened to me, I wore them with laces tightened up tighter than normal and for an hour or two max. Then built up time used and after a few days/weeks I could wear then all day and slacker ( I usually have shoes fairly slack unless particularly needed for what I'm doing).