You are not alone I have had issues with these primers exactly the same as you, I stopped using their small pistol primers back in the 1980s I had hundreds of Sako cases & they would not seat flush, I actually broke the bottom yoke on a Dillon press seating these, the answer was use different primers, end of problem. I still use that Dillon after 35 years, I only use large pistol primers these days & again I cannot seat CCI primers in some cases so I don't buy them, strangely enough I can use CCI rifle primers with no trouble but I only use them if I can't get any other brand, however I use a pacific single stage press for loading rifle ammo. My advice try other brands, if they seat O.K. end of problem.
Elwellaxe.