nonseven,
I had primer strikes like that last week with Remington Green Box ammo I had lying around, and wanted to use up. (I mostly use Winchester White Box or Blazer Brass for practice.) The rounds fired, but I didn't like the look of those primers. So I fired a couple of those Remington rounds in my Ruger SR9. They fired but looked strange too. There was a small indentation in the primer, but not near as deep as my Winchester ammo.
I then fired a couple of rounds of my carry ammo, 124 gr. Speer GDHP thru my R9s. The resulting primer strikes looked okay like your second photo.
The only other time I've seen flat primer strikes like your photos was when a little shaving of brass got stuck in the firing pin hole of my R9s.
You might want to pull the slide off your R9 and manually push the firing pin forward to make sure there is nothing stuck in the hole or to the firing pin.
Steve