This is hard to answer as I don't have access to your graph, but this may be linked to the Color Correct box being connected to a box with a dotted cord inside the Cloud FX graph. The dotted cord itself is not replicated outside a graph, but this does not mean that its behavior does not apply.
You can read more about the signification of a dotted cord in the Working with Texture User Guide.
The connection between the Dest Input Pin and the Texture Buffer is dotted. The dotted line means the box writes back into the previous box. This is an advanced process to avoid the creation of multiple render target when unnecessary.
This process is used by a few boxes, including the Blend box, the Scene Renderer box, the Draw Surface box and the Surface Mapping box. If you have one of these boxes in your Cloud FX graph, with the Render pin exported or connected to an extender with an exported pin, you can use a Format box to isolate the dotted cord from the Color Correct box. This way, your cloud effect will not spill behind your rain effect.