I'd probably go back to your fitter and see if he/she can help out. It might be the cleats need to be moved and/or you need different insoles or you might need wedges.. or...?

Most reputable fitters would want you to come back and let them know of the problem so they can further tweak the fit for you. The shoes are likely much stiffer than your other shoes so perhaps they aren't as flexible to the various motions of your foot during the pedal stroke. Your foot may also have to adjust to this. This is all postulation on my part, however since I'm not a fitter by any stretch.

If you trust your fitter I'd go back to them. If not, then as others have mentioned go thru some trial and error with the various options out there. My friend had the same issue and actually went to a podiatrist who also happened to be a cyclist.. or a triathelete. She found that at least gave her clues about her feet and some direction on how best to resolve issues.

Good luck!