Could your boots be a bit too large, or a bad fit, or the soles to stiff and inflexible, causing the back of your heel to move up and down in the boot as you walk? That's what it sounds like to me, though I'm no expert, I'm fortunate enough never to have had boot problems, other than a pair that were a fraction too short for me, resulting in black toenails after a multiple-day walk.
Beware chiropodists! I went to one with what I thought was a thorn embedded in the ball of my foot. "It's not a splinter," he said, "you've got a baby corn. I'll remove it for you." I paid him £28, but returned 4 wks later as the problem was the same. This time he said it was a verrucca (have I spelt that right?) and recommended treatment that would cost £150 to £200. "No thank you," I told him, whereupon he demanded another £28 consultation fee, following which we had a big row.