I can't imagine the padding being the issue. Heck, my Bull-Pac frame pretty much has no padding in the belt and I haul 100lb loads with it all the time. But I also lock it in above my hips, not around them.
I have experienced hot spots on my hips from different packs too, and i found that the merino shirts i usually wear have seam that runs down right inline with the points on my hips bones. And after a little bit of hiking those seams were the culprit. Ice breaker merino shirts were the only ones i could find that didnt have that pesky seam