I have experienced similar issues. At first I was using an RCBS Rockchucker with the priming set up on the press. I tried pressing the primers so hard I was picking the bench up, and still not getting the darn things to seat right. This was not consistent, as different brands of brass were problematic, and it was only a few out of every hundred. After discussing the problem here in TFL, somebody mentioned a "primer pocket uniformer." I got one and that solved the problem. Some primer pockets just seem to be undersized and/or shallow. Using that little tool cleared it up. It is a kind of time consuming, but worth the effort.