Check with Nordica and see if the liners are remolded. If so, pack out your ankles and remold them to see if that helps. Did the liner happen to get folded over during the molding? - that would put extra pressure on your foot. Take the liners out and see how think the liner is in the areas around your ankle. If it's paper thin, there is not much you can do to fix that, since you already tried to punch them out the shells. If you are willing to spend the money, get a pair of intuition liners. You can remold them 6 times (incase you make a mistake the first time or they start to get packed out after a couple of seasons. I got them a couple of years ago and they fit like a second skin and are warm as hell.
They were done properly. The issue is the shell. The hinge point between the upper and lower shell sits right on my medial malleolus. It was mildly uncomfortable when I first tried on the boot and after molding as well. Haven't owned Nordica before and have not had this issue with other boots prior. Fit well every where else and the $350 price tag had me sold figuring after breaking the boots in the problem would go away. It has not and you really can't punch out the shell where I need it done due to the hinge.
It's painful, but not unbearable. I'll get a bit more of my money out of the boots before moving on.