Yes, maybe on a linux machine I have laying around. I usually bring my work laptop home but I have no admin rights so have to use the one portable version I found online.
So it definitely had something to do with another copper fill, also a ground fill on a different priority level and different constraints. I tried to jiggle the two fills in relation to each other and managed to make the fill appear/disappear in the 3D viewer with the jiggle of 0.1 mm in a given direction, but it really never gave me a clue to what was causing it.
It would be nice if you could test this in the nightly builds.
I do not recommend 3D Viewer for copper inspection as there may be issues or differences like this, proper inspection must be done with gerber viewer.
As a suggestion maybe you ca help kicad by simplify that overlap zones