Its funny that you mention this because I just bought last years Burton Hails from the snowboard show and had the exact same problem.
They felt great at the store, and for the most part great when I was wearing them at home, just after a while they would make certain spots in my foot hurt. I ended up just changing the kind of sox I wear with them, as well as ajusting the way I tighten them. This now allows me to wear them pretty much all day long without any problems at all(already have actually).
Sorry if that sounds like an obvious fix but its something you may wanna try and see how it feels. Most snowboard shops should at the very least give you store credit, if not money back.
I bought a brand new snowbaord one year only to find out the next week that the shop I bought it from got a bigger size which would have suited me perfectly. The next day I brought in my board and exchanged it no questions asked.
Shredding the ice coast, one hill at a time....