Do you use SH3 Commander? Did you roll back before looking at scene.dat? How did you view the dat file.
I think a solution would be to get a 'clean' copy of scene.dat from one of the separate atmosphere mods.
Are you using GW1.1a auto installer or the patched version?
N.B I have both versions of GW so could post the correct dat file for you if needed.
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