Josh,
Primers normally require a little bit of crush. This is called setting the bridge by primer makers and "reconsolidating" the primer by the military. The idea is that the primer anvil comes a little tall and when you seat the primer it should squeeze the anvil into the primer by about two to four thousandths of an inch.
It is common on progressive presses for the the primer to seat when the press handle is at low mechanical advantage. This is to let you "feel" the firmness of the primer seating effort. The problem is that some primers have burrs and are harder to seat than others, so you can think they are seated when they are not. I have this problem on my Dillon Square Deal. Also, some cases have crimped primers, and if the crimps are not either cut or swaged out, then primers can fail to seat fully.
What you want to do is gently measure the height of a dozen of your primers to get an average reading. Then do the same with the depth of your primer pockets. Be carfull making this measurement as it is easy to get too short a number off a caliper depth probe. Usually you get a better result by measuring a small pin that fits into the primer pocket, but not too loosely, then the case length, then putting the pin in the pocket and measuring the combined length and subtracting it from the sum of the pin and case lengths. This gives you a pocket depth. If four thousandths smaller than the primer height is greater than the primer pocket depth, then pocket depth uniforming is in order. If it is, you are likely just not pushing the primer in firmly enough and need to solve that mechanical problem. Swaging or reaming the pockets, even when there is no crimp, often makes primers seat more easily.