I just wanted to add that I was having the same problem. After reading this thread, I looked in my scripts file and found the TrueHaze.lua, so I moved it over to the Scripts(disabled) file. Problem solved.
Also, before permanently resolving this, my work around was moving the settings slider from HDR to HDR + SSAO, or vice versa, and it would fix the issue I was having with the clouds, until the next time I flew.