I had that exact problem with my running shoes when I was picking them out myself. Went to a local running shop and the owner analyzed my gait, said I was in the wrong level of shoe (i was in a support shoe and needed neutral). Switched the shoes a few years back and the problem was solved for me. Now I just let him pick out my shoes and reccomend insoles for my boots if they bother my feet. I know everyone's issue is different, but checking into this might be an easy start for you.