Something else to consider. In your original post you stated the intensity is .007A. Boeing generally allows a wide tolerance range. -0.002 to +0.005. So the allowed range would be .005-.011A. You might want to find out what the "intensity" is is of the process. If its at the high end of the range target the process to the lower limit. Perhaps impose your own tighter limit say .005-.008A. If that doesn't work you may want to peen the parts a second time at a substantially lower intensity but cutting the air pressure 50%. This will help to knock down the "high points" of the peening dimples. I suspect when you're measuring your picking up these points. Think of it as a peak of a wave but not the level of the sea.