Well they are as fully seated as I can get them with my press. Not sure if some primer pockets are not as deep as others or if there is some crud in the way or if my press needs some adjustment that I am not familiar with. I am optimistic as the 25% that are not flush are barely not flush and you really have to examine them to tell, at the volume that I shoot I really want to avoid hand priming.
Are you cleaning the primer pockets? I have a small round ss brush on my prep station that all of them get hit on.