Hey, Streetwind! I like your profile pic, by the way, it's quite unique. I, too, encountered this strange thing, also on Laythe and Jool. It's the resizeClouds config file in Sigma Dimensions that causes this (it's actually supposed to do that, for reasons). Rather than finick with it, I commented out each line of that file, which you can have, here (disabling the file will prevent you from having to resize your clouds manually each time you boot up KSP): https://drive.google.com/open?id=0B2RU6X5cw9o2cDlaZmM3Sm1xeGM
After that, just boot up KSP and patiently resize your EVE clouds on each planet (which you can do by pressing Alt+0 to bring up the config menu and finding the "CloudsManager," then going to Eve, Jool, Kerbin, Laythe, so on and so on) in the tracking station). They'll go from this:
(Yes, my Eve clouds are pink, I like them like that.) Back to this!!:
Hope that helps!!!