I use FSX boxed and I'm having an issue I used to also have with P3D, but I just fixed it by clearing my shader cache. In this case, my FSX shaders have not been modified (i checked the modify date, all of them are which from 2006 ~2007) and I've tried clearing my shader cache to no effect. 

Rex Sky Force 3D + 3d cloud models, Default Thunderstorm weather preset

I use ENVTEX sky textures as well as REX Sky Force 3D (32 bit version) for the cloud textures. I noticed even with ENVTEX textures, the clouds still have different colors.

ENVTEX Clouds Default cloud models, Default Thunderstorm preset

Is there any way to fix this?

Fixed it. I had to use an alternative cloud model.

Great you managed! Also keep your GC driver updated.

Berlopez