Not sure if it was there in previous builds but selecting weather other than "clear" displays this huge plane in the skies instead of clouds. It doesn't matter which track is selected. This is part of my trace file which may have something to do with it.
Those textures are in the rFactor2/Core/Shared/Sky.mas file. There is no Sky_b.mas though, but maybe you could try copying Sky.mas into the corresponding folder in the ModDev folder structure and see if that works? (I don't have ModDev installed at the moment so I cannot test)
Copied the Sky.mas from core to moddev, and added a renamed Sky.mas to Sky_b.mas, no change, don't work. Copied the Weather.mas from core to moddev, and added a renamed Weather.mas to Weather_b.mas, no change, don't work.
I did a really ugly hack to work around this bug. Grab http://racehub.se/rf2/moddev-sky-hack.zip and unzip its content to the .../rFactor2/ModDev/UserData/Log/Shaders folder. That should allow clouds to be displayed. Hopefully ISI can fix this bug soon. (And ModDev should really be part of the unstable testing, imho)