I haven't had this after running but I do a lot of high altitude trekking and climbing/mountaineering. I found I got something similar after wearing my boots for a over a week.
I changed to a better brand of sock with a inbuilt wicking liner. Maybe changing your socks to a full wicking set may help? Also my new boots have a B3 rating which means that its a fully stiffened boot which doesn't move or bend. Following that logic through, maybe you need a new shoe fitting?
Not sure how much help that was 