I think I found problem. Paint layer contain option to be painted on various channels, apparently default in my case was to only work on color (now I know where to look).
Q: why by default that is setup only for color channel, not for all of them? - feedback to make it by default on all channels.
I think its single time thing that everybody need find to know later. I suggest to make small update to documentation
"A smarter way to use the Clone tool is to create a painting layer and set the blending mode of all the channels to "Pass through" - and add info "ensure that paint layer is setup on all channels."
But confirm on your end that was a issue as well - I work atm on 11 variation of project with plane from blender.