I've been walking for nearly a year. I do take time to stretch afterwards. The pain seems to come on when I've been walking a bit over a mile. It's a dull ache, and not enough to stop me from walking. It goes away quickly after getting out of my walking shoes and carrying on with normal activities. My walking shoes are new. No problems with blisters or any binding issues. I suspect weak ankles or possibly a stress fracture.
It could be a stress fracture coming on. But I suspect that it is your shoes. I know you said there are no binding issues, but perhaps you should try leaving the laces off the part of your foot where the pain is. So, make a box shape with your laces in that spot and then lace as normal at the top. If this causes your heel to slip, you can make a loop lace, which is the best way to tighten your shoe to your heel. It is hard to explain but if you go to your local running store they should be able to help you with this problem, without trying to sell you anything.