I went back and deleted the conf.ini file +cache and tried again. Still gone. I have a few missions with clouds i try all the time. Everything is dull and flat no matter what time of day.
One weird bug I noticed attacking some He111's at 4:00 in the morning was how completely out of sync the brightness of the "wounded" red texture compared to the outside environment. I think that "wounded" texture is not affected by the general luminusity of the environment.
I hope they can get it all fixed again.