It was not meant as a suggestion for solving your problem, but as a suggestion in general for rendering
Setting up the renderer this way makes your rendertimes unnecessary long, think this setting will save you in this case at least 50% of the time.
Also, I saw you have a compute terrain, then base colours and then a compute normal which isn't needed at all. Remove it, and save even more rendertime
I just used the setting "raytrace everything" and that works, but the terrain looks really messed up now.
I think this is a bug we're dealing with. First the clouds sticking through and secondly the odd results using raytracing on everything.
Martin