@ WAS: Atmo and shading is deferred (Render node).
@ Matt: I tried again with the 3D Preview closed, no pausing, no other previews open.
I am still getting the same results. The cloud nodes come from the preset pack "ragged_storm_clouds" ("v2"clouds), so maybe that's it. I'll try again with the current "v3" clouds with settings to duplicate. If that doesn't work, I'll probably just ditch the effort and move onto something else.
Thanks anyway.