I had this problem
for me it was related to the scene.dat file. I had again the clouds when i substituted that file with the scene.dat contained in the environmentcolours mod (you find it in the mod forum) and rollback from sh3comm.
I dont know if depend form sh3comm, but i made the sobstitution in the midlle of a patrol and the sky from a perfect blue sky became full of clouds ..... i try to reinstall the sh3comm eand the sky again was empty, i rollback and re-put the env scene.dat and again clouds.
It's an empirical solution, but it works for me .... but now i have the moon with a background square (it is a difect of environmentcolour mod.) i dont know if i can sobstitute the moon tga file ... at the moment i didnt find any solution in the forum ...
i hope this useful
sorry for my english
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