I haven't tested with your .ter yet, but I think I can see the problem. The Strata and Outcrops Shader usually makes large displacements, as it is in your scene. As a rule of thumb, anything that creates significant displacement should always be added to the Terrain section, not the surface shaders. In other words it should come before the Compute Terrain node. If it comes after the Compute Terrain node, it won't affect the other shaders in the way that you'd usually expect it to (surface normals and texture coordinates), and it won't be taken into consideration by the populator which is usually connected to the Compute Terrain node.
You can avoid the populator problem by changing its "terrain shader" connection to point to the very end of your shader chain. This might be a good idea for your scene because there are other shaders which are affecting the displacement too. But really the best advice to avoid various other complications is to add your Strata and Outcrops Shaders or any other shaders that add large displacements to the terrain section, before the Compute Terrain node.
Matt