One final adjustment that I have found necessary (in my very long TWO WEEK career of fidding around with this stuff) is to adjust the HORIZONTAL Cloud Plane ALTITUDE. Many times a Horizontal Cloud Layer at 3000 feet is too LOW and it will CONFLICT with your VERTICAL Cloud Planes. You will most often see this as BURN MARKS or other COLOR NOISE on the Tops of the Vertical Cloud Planes.

So- MOVE your lowest Horizontal Cloud Plane up to around 9000 feet or so and the Conflict should go away and the Clouds will all Happily Co-Exist with each other!