do custom footbeds need to be worn in?
It could be your binding angles or strap locations too. I know I had a burning sensation right at the balls of my feet and making a few adjustments to my bindings I think I bumped my front one outwards three degrees and I started putting my toe strap over my toes. Rather than on top of my boot. Seems to have helped quite a bit.
It comes and it goes. Get it while it Lasts.