Is it your conclusion..? Your posts put me in suspance... I was thinking I was getting close to the solution...!!
However, the difference should be between the stock and GWX scene.dat, probably in those parameters that control clouds behaviour/resolution/appearance..
We need a guy who knows very well that file!
thanks anyway for your attempt!
Edit.
I compared the two files by using S3D.
at the node 44 there are clouds parameters. The stock 3D model (subnode 39) has 2 UV Map channels, instead the only one Map channel in the GWX version. Can be it the difference?? Maybe my video card wants that second channel... I don't know!
The other things related to clouds parameters seem the same..