James;
Large rifle primers and large pistol primers are not the same height, by .010".
I had been using one brand of .44-40 case for several years, got new cases of another brand, the first case I primed in a Lee hand primer would not come out of the tool, I finally had to use both thumbs worth of pressure to crush the primer enough to get it flush with the base and get the case out.
Check the primer pocket depth with a caliper and make sure what primer pocket you have, large rifle or large pistol.
Don