When I quit to main menu and reload, it seems to be applying that atmoTopLayer thing all over again. Here's what it looks like after 4 and 5 reloads with the following settings (based on original KScale64 and improved for the latest SigDim version):

SigmaDimensions
{
	// Base Settings

	Resize = 6.4
	Rescale = 6.4
	Atmosphere = 1.33
	dayLengthMultiplier = 4


	// Advanced Settings

	landscape = .50
	geeASLmultiplier = 1

	resizeScatter = 1
	resizeBuildings = 2

	CustomSoISize = 0
	CustomRingSize = 0

	atmoASL = 1
	tempASL = 1
	atmoTopLayer = 1.4
	atmoVisualEffect = 1

	scanAltitude = 1
}

This makes things difficult and requires the full game restart to make everything work properly again.

thanks for the report
It's an easy fix but I have another more difficult bug that is slowing the update.