It's actually two textures that are in the same spot fighting over dominance. (The engine can't determine correctly which face should be shown, so it differs on each different render.
A simple solution is to put one of the two meshes (or the part that conflicts tih the other mesh) a fraction higher (about 0.5 to 1 inch is often sufficient, and hardly noticable on large scale.
It often occurs when using alpha vertex painting on copies of meshes.