After 1 year I got rid of the Square Clouds. 256/Big. This combination seems to be stable. Square free, less strutters.
I tried also different conf.ini settings, just realizing, it had no effect at all.
I did a small test:
If you disable in TexFlags.SecondaryColorExt=1 to 0 you can see the squares not being transparent or 3D, while the clouds are. This removes the 2D Sky-Blue/Highclouds and turns it into Black. Don't do this, unless you really need to, it sets all your GFX settings back to default, so keep in mind.
Highclouds for me have no effect on these Squares.
They seem to be be frequent in Cumulus Original and RA size, somehow they disappear when selecting big. Even if they seem to be non existent, they can pop-up after re-starting game in those sizes.
A promising visual effect, I really hope Bender gets rid of the Squares, get this a stable basis, just imagine it working in all combis like we have now and with our future AI not seeing through clouds option. You could just hide in a cloud or see them as an advantage, no more Chuck Norris AI. ATM. it's just a visual effect, but later it can be the creme on the ice towards immersion and beating AI.
Thanks Bender, keep up the work