Legal is on the right track here I think. It does sound as if a surface never in the instep is being pinched. The good news with these little surface nerves is that they general recover fairly quickly when you relieve the pressure. Do your inner liners have the velcro strap at the top of the shin where you can tighten that up? If so, you can leave the liner laces a tad looser and compensate by tightening this strap more.
Another thing you can try if all else fails is to place foam padding on the liner, under the lacing to help reduce this pinching from the laces. giving a more evenly distributed pressure over a wider area of the instep.
I'm going to try that foam protection! That's a great idea. I'll test it out in the next week and report back. I might also try a custom boot fitting at a shop about an hour+ from where I live.