In reply to Darkskys: I suffer from this pretty badly too, but i've just been putting up with it, even in walking boots after a long day scrambling the balls of my feet feel like they are screaming at me.
Recently i just took an old pair of liners from my La Sportiva running shoes and put them under the stock insoles that come with the Nepal. Seems to have helped a little bit so far but only used it on three or 4 hill days so we'll see.
I think lacing techniques can play a bit of a part with it as well, although the laces on the Nepals are pretty crap and i need to re tighten them at least three times, seems simple but not with internal gaiters, bungees and crampons on.