Sounds like you need a wider boot. I had a similar issue with some 32 boots where they were too skinny. Tried thinner socks and even got to a point where I took out the liner and cut some of the supportive materials away from my arches and even that dident work. Still had intense foot pain and had to break every 2 or 3 runs.
Ended up getting northwave boots and the problem went away.
You could also try using the arch supports in your daily shoes so your feet have more time with them.
I actually have the blues in my daily walking shoes with no problems. I have been riding for half the day up in whistler today without the superfeet and theres a lot less pain. Pretty much no arch pain.