Hi Ken,
Just a wild guess here.
Could the raw counts per pixel be close to small integers, e.g., 1, 2, 3, etc. photons? In other words were these pixels acquired with a very short dwell time per pixel, so only a few photons were captured? Take a look at the net intensity maps, and look at the count rate...
By the way, what was the pixel dwell time and beam current?
john