City Lights for Kerbin and Clouds for Any planet you wish! The config file can be modified to add any number of cloud layers to any planet.
Going forward, I will no longer even RESPOND to posts that don't have a good description, a screenshot (if applicable) and a log file. If you don't do this I know you haven't read this, and if you don't read this, I can't really spend the time to help you if you don't attempt to help me.
HOW TO GET HELP: http://forum.kerbalspaceprogram.com/index.ph
Ah I think I may have found the cause. In the Texture Configs, if you specify to use the same file for two different cube maps, if doesn't render the ones higher on the entry list.
For example, the config used for the screenshot above was:
OBJECT
{
name = PoodsOPMVO/Textures/aurora
isCubeMap = True
texXn = PoodsOPMVO/Textures/blankchannel
texYn = PoodsOPMVO/Textures/auroraTest
texZn = PoodsOPMVO/Textures/blankchannel
texXp = PoodsOPMVO/Textures/blankchannel
texYp = PoodsO