Unchecking "Atmo/cloud on background" will have no effect if the background has an alpha of 1. "Background" means any pixels with 0 alpha. With your image map shader connected to the background, this is now a surface just like any other, and the renderer does not know that it's meant to be the background. It may be possible to set the alpha to 0 by chaining a Constant Shader before the Image Map Shader but I forget whether this works. I'll try it later.
Since you're replacing the background, isn't it better to disable this object/shader anyway?