Hi,
Well, RailClone surface tools are a little limited at the moment. Rather that follow the polygons or the UVs like a panelling tool, In RailClone, geometry is projected along the RC object's local Z axis until it hits the surface's geometry. This means that it only works well when the face normal points towards the RC object. Any polygons with faces that point away or overlap will not work well. Sometimes, you can get around it by spitting the surface and using several RC objects with different orientations.
For these purposes, using the Forest Pack in the UV mode would be the commendable way.
Best regards,