Materials are instantiated and cached at runtime for better performance and because Nature Renderer has to set a few additional settings for your materials. This means that if you make a change to the (original) material then these changes are not shown unless you explicitly refresh the materials.
You can use NatureRenderer.Refresh() to apply and show the changes:
using VisualDesignCafe.Rendering.Nature;
GetComponent<NatureRenderer>()
.Refresh( NatureRenderer.RefreshFlags.Materials );