Btw you imported some textures in SkyT as masked by default (when you put them on any surface it will be masked no matter what and it can be hardly selected), they were not masked by default, they had black borders. Try unchecking them so it is like original?
Its a bit unclear to me now if the resulting textures are correct now or not. I would like to see the original utx files, so i can have a look at them, and if needed i can re-asemble them. When done i can offer them as official files in the texture downloads, which would also make them aplicable for S3TC updates.
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