dents shouldnt stop em, but ive heard of people having pierced pipes or pipes that were either not vacumed or gassed.
Would certainly cause this type of problem, as without the heatpipes you have a very small cooler indeed.
To check contact issues is pretty easy; place a small blob of AS5 in the middle of the IHS and mount the cooler as vertically as possible (i.e. dont slide it on etc etc). Clamp it down as per usual and then take it off and see the AS5 mark left. if it stays very central (concaved base) or spread to one side (uneven base) then thats ya problem.