Haha Nice work Oshyan with the test.
I have had same trouble and solved it like Oshyan suggests, but I would also like to make the clouds one color without the control I have to have with setting the sun and so on also. If you go in and make the clouds one color in the Atmosphere Tab, that should be all to make that happen, but..... So I personally would like to see a color table on the clouds that would effect the clouds and not the surrounding inviroment at the same time. I do see why they did set it up this way, but no room for the insane acid Psycodellic skies with it yet. So maybe they have that on the ta-do-list maybe?
DT