Let's let this go to a ticket, but some parting thoughts:
You've got a fair amount of third-party plugins and scenery installed - I think I see signs of HD Mesh, which may be consuming your available memory. If you haven't already tried it, see if temporarily removing your add-ons and custom scenery brings your clouds back.
You're also flying in a very stormy area, which further strains your system's resources. If you manually set up partly cloudy conditions, do the clouds return?
I know you've got a decent system, but it's still possible to overload it with too many add-ons.