Lower clouds disappeared? How can I get them back?

I do not have Truesky disabled, I did not change any settings that I am aware of. I even went back and redid all my weather/sky files, but I seem to be missing all my lower clouds somehow?
I used to have ones that touched the tops of my mountains, but now they are just… gone. The image posted are the clouds I am refering to. They no longer exist on my map, and I cant figure out why.