Join Date: Oct 2013
Location: Stuck in Ohio. Rockin it.
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My best guess regarding your boots is that they are too small. If they have wiggle room in the instep you're not going to get proper support from the inner laces. It'll create a pressure point because the inner laces will be tighter than the rest of the liner. Try loosening them a bit or don't even tighten them at all for a few runs. You will take a hit in response, but if the sore sport goes away, you'll know that's the source of the problem.
The other guess is you may have a technique issue. You may simply be fighting the boot. If you're pushing down into the boot with your toes on either edge, it'll push your instep into the tongue of the boot, which will cause you a lot of pain very quickly. This can be hard to spot without coaching because you can do it passively and it wont interfere with your riding, but it will cause a sore spot on the front ankle and instep. A quick lesson with a half decent instructor and they will be able to point it out in your first few turns.
Edit, what are those orthotics doing for you? Arch support? Cushioning?