Same problem for me. (Vanilla and Multiplayer)
I have clouds and after sleeping there are no more. (Host User/Linux) Another person on the same server (Joined User/Windows) sees the clouds, but with slight bugs. After save and load it works fine. But I also have the additional problem that we don't have any rain near our house, even though there should be frequent rainfall.
But I don't know if the two things are connected.
However, it seems that the problem only occurs when I open the game to the Internet. If I start the same Map without LAN/Internet, then it works.