Just to update on what I wrote here. It's a problem with the Nikon not the Atomos. I did several tests directly to Nikon in Flat mode and the problem is there as well! More enhanced in 12 bit N-Log.
Here's my tests...
https://youtu.be/1w69jYu-cIU
and here's the HQ version for download...
https://www.dropbox.com/t/vNjH4yBSImvAhK8H
Hope Nikon can / will fix this. Very annoyed.