I've never really had any pain on the top of my foot, but a few things to think about.
How tight are your lower laces? They could be too tight, or the liner could be too tight causing that. Play around with that part of the boot and see how you feel.
The other thing it could be is that you are cranking your bindings too tight. That can cause pain on the top of the foot also. Think about that the next time you strap in.
If it continues to bother you, it may just be that the boots aren't right for you. Everyone is different. Whenever you go to buy boots, try on as many as you can.