What you're describing, primer flattening, is associated with over pressure loads.
I've always suspected that there are other factors that may play into it, such as a run of primers that have a softer than normal metal forming the primer cup.
Primer flattening also can happen when a bullet gets shoved back in the case from being in a magazine and loaded (chambered) a couple times, but not fired. The impact of hitting the feed ramp drives it back into the case. The OAL is lessened, but more importantly it drive pressures up, sometimes dramatically. I see a lot of people unload and load back up with their carry ammo when coming out of the range. They load the same round that came out of the chamber back in after a range session. Not a good habit, IMO. Myself, if a bullet has been chambered, it gets shot at the range (after being examined for set back or other damage), never loaded back in and carried. Bullets are cheap, guns aren't.
I wouldn't expect to see primer flattening from excess pressure with "normal" factory 9mm SAAMI spec rounds, but have definately seen it in +P+ and SMG handgun caliber ammo. Were it me, I would definately check the ammo and make sure some LE stuff didn't find it's way into the Rohrbaugh, or maybe a "set back" round or 2 got fed through.
Hope this is of some help.