Today, I have found out that the clouds bug which causes the clouds to disappear is also related to saving. When saving a custom made planet with clouds, the clouds completely disappears when re-spawning the saved planet. Any planet that contains water must have clouds if there is an atmosphere, so the clouds should load when re-spawning the planet.
The cloud disappearance bug must be fixed in the next update because its very annoying. When you have clouds turned on in both the temperature tab and or the climate mode tab, the clouds do not show up when the custom made planet has been re-spawned in a new simulation. Please fix the cloud bug.