I am not quite sure what is causing your issue but I ran a test and was able to see similar results.
What I did was create a material similar to yours with 3 layers. I then applied that to the landscape. I then painted with one of the layers. What you see is a preview of the landscape as it thinks it should look. Usually this is black. When I painted I saw very large squares where the engine tried to estimate how your texture should look when painted. What I do is paint the entire landscape with one main paint layer. Then, I build the lighting. After that, I painted with a smaller brush with a different layer. When you first paint with a new layer the shader will recompile as you are adding new data on the map you are on but as soon as it finishes everything should paint as you would expect.
