As I already said I fixed it by deleting all the unnecessary configs from GameData/BoulderCo/Clouds. You have to leave only one of them or you will get multiple clouds. I have TextureReplacer, PlanetShine and so on (everything which was required for KSPRC, latests versions). I didn't replace the stock assets file (it would break stuff until updated) and RSS configs and etc of mods which I don't have. I also added -force-opengl flag to my game executable and my game with >40 mods eats less 2gb of ram (or a bit more).