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When I have "Invert Background" on, the "Background" settings in the view are also inverted when using the "Sky" setting. Meaning if I use a Ground Color of green, the ground color is inverted to Magenta. This isn't true when I use the "Gradient" option, however.
This has been submitted to our development team for further investigation. In the meantime, I would suggest setting the Ground Color to Magenta when using the Sky Background, as the result will be Green.
I am sorry for any confusion or trouble it causes to your workflow. Please let us know if you have any additional questions.