I can certainly look into it, but it's a bit like searching for a needle in a haystack. Do you know the name of the cloud file in question? Do you recall if the weather was described as Light, Variable, or Scattered? If you haven't run another mission since then and you use Jara's ME, you can open his mission editor log file and near the end of it, it will list the cloud file used for that flight. All of that might help me narrow it down. Also, the problem may be due to the drawing of the texture itself, which I lack the ability to change.
As always, thanks for the comments and thanks for using the mod.