Checking out if it can be about collisions but I do have them as far as I know - also it’s walkable ingame so yep I would think they are okay.
So I’m not using the paint layers but texture maps instead (in this example a black and white checkerboard)
Now I see what you mean with the layer, if I add one like if I was using it, it doesn’t change anything anyway 
More speaking screenshot:
Just tried:
- Leaving the landscape where it is when you create it rather than moving it to 0. 0. 0. - Same result
- Painting some height to ‘refresh’ the scattering or whatever but didn’t fix it neither.
Just tried:
Having a paint layer (even though I do not intend to paint anything) : same result
BTW, It seems I can’t erase areas even when specifying target value: 0.