Lately the Compute Terrain has been having issues, I'm not sure what version this came about, but it is no longer conveying correct texture coordinates, or positions for secondary displacement, and it no longer "Blocks" a smoothing effect of a surface layer. Before, you could have your small scale displacements after your Compute Terrain, and than use a Surface Layers "Smooth effect" to mask out those small scale displacements. However now it will smooth right on past that Compute Terrain.
To fix both texture coordinates and smoothing, and displacement alignments, I've had to add to my Default Project a Texture Coordinates from XYZ after the Computer Terrain.
Take this example. Here we have a river 30m wide river, with 1-5m main stones on some dirt... If I enable Smoothing effect to mask out the dirt/floor displacements, it masks out the entire river above the compute terrain in the main terrain displacement.
I've noticed I've needed to add a Texture Coordinates lately for textures, just didn't realize it ran so deep.
Discovery: I discovered this by opening a old underwater river scene in 4.4.44, to be greeted with no river! :O That was certainly not how it was saved or rendered originally.