I've been having this random issue with materials appearing misaligned and on the wrong surfaces:
I have figured out that if I select all of the faces with each material (stone, then moss) and move the whole uv map slightly by hand, it usually fixes the error.
This, for me, solved an issue in Substance Painter, my formally mirrored mesh made in Blender (modifier applied and fresh unwrap) had a problem when I tried painting on a formally mirrored part of the mesh. The height would not show in the 2D window and the very same parts looked like in the bake AO was reversed in the 2D window. In the 3D window all looked fine. TY Old Vamp!
This will be part of my workflow from now on, just like CTRL-A ;)
What also fixed the problem was exporting without tangent checked on FBX export.
