Weird issue when manually painting terrain on neighbour

[Hellbourne]

I am having an issue, when painting textures manually on my terrain (touchups, extra detail) Everytime I paint over the line onto a neighbouring terrain, the neighbouring terrain goes black and loses all textures, when I ctrl Z to undo it converts the entire terrain back to white, the only way I've found to fix this is to user the biome tools and repaint the entie world, losing all of my progress and I have to repaint until it happens again!

[Bryan]

I have seen this before and is usually an issue if the terrain goes past the texture limit. 
What could be happening is that for some reason it's duplicating the textures on that terrain. 

Can you tell me, is this a multi-terrain setup with Gaia or the Neighbor Terrains through the standard Unity terrain system? 

Can you check to see how many textures are on the black terrain? If so do you see any duplicated textures?