How tight are your boots tied? How tight are you strapping your bindings down? I have flat feet too. I use Dr Scholls arch supports. I dont like to tie the 'toe' part of my boot that tight, but cinch the ankle/calf part down fairly tight. I also use toe caps instead of the old school over the top of the toe strap which seems to make a difference. I go pretty snug but not as tight as I can possibly go on my ankle strap.
I also prefer a thinner (Volcom) snowboard sock as opposed to a really think snowboard sock that I used to wear. A little more room for my foot to move around rather than cinching it down super tight and forcing the flat foot scenario.
To to Walmart and try that Dr Scholls foot thing. They're like 40 bucks. I really like them. If you arent happy with them you can send them back and get your $ back. Worth a shot.
I didn't tie the boots any tighter then I did last year. The SOLE thin sports did a great jobs last season. I think I paid $45 for them. Not expensive and really help my foot pain. I'll be going back to them if my pain doesn't go away.