Always make sure you have a good footbed in your boot. Your foot was designed to flex and walk, not be stuffed into a plastic cast. If your arches collapse, it pulls on the rest of your foot/leg as well and this could very well be the cause of your problem.
Also, try putting some everyday arch supports in your everyday footwear. You do the most help or hurt to your feet in your everyday shoes, whereas you are only in your ski boots for a few hours at a time.