Interesting. If anyone finds out any more on this I'd like to know, as it may help me improve RAID Weathers. Anyway, I may do some experimenting on this to see if I can figure anything out.
Long shot, sorry to ask (just saying since some other users reported similar things to me about this), but are you sure you have "bUse64bitsHDRRenderTarget=1" enabled in skyrimprefs.ini under [Display].
EDIT: just noticed one of you is the bethini author, so lol, sorry for the above question haha (i dont use bethini tho).
OlivierDoorenbos's post in Looking for the source of cloud/fog/smoke/wind coloring - Weather & Image Space was marked as the answer