Something similar happened to me already with a couple of boots, namely that my feet started to hurt properly, but the boots weren't too small. As far as I could figure out, the problem was in the arch of the inner foot of the boot on the outer side, so not in that anti-flatfoot bump under the inner side of the foot but in a very slight (but still too pronounced for my foot) bulge on the outer edge of the foot.
Solution: other boots. Once I (more to identify the problem) tried cutting out the inner insole in that part, and my feet didn't hurt anymore that way, but the pressure on the edge of the cut part was a bit uncomfortable when walking, on longer walks it would probably blister too.
Unfortunately I haven't learned yet to recognize this problem in the store when trying on, so it happened to me twice, not just once. So the advice is mainly -- if a certain brand of boots doesn't cause you problems and their last fits you, buy the same brand next time too.
(One would think that if someone has flat feet, a similar problem could be caused by the bump on the inner side of the foot.)