I had a similar problem recently where color was not appearing on lower, more sloped parts of stones and it was due to a particular Slope key setting.
If you have set a maximum slope angle to limit the stone layer to flatter areas of the terrain, the Slope key used may actually end up applying to each individual stone so only the low angled upper parts of the stone receive the color.
You could try a little crop test using each different Slope key (Final normal, Terrain, or Planet/object normal) and see if one of them corrects the problem.
Example : two renders - exactly the same scene, except for using two different Slope key choices in the stone distribution shader.