I have noticed this since the days of WoM. Often when you start a game with a previously created nation, one that you have played with previously, not a brand new created one, their second color turns to white. It's annoying as shit, and when I open up the file to change the color, I don't even see an entry for a second color anywhere. Please fix this please.
I'd love to see this fixed too. My experience has been always that starting a different game with the same faction results in this.
In the meantime you can get back your secondary clothing colour, and the primary and secondary building colours if you want them by opening up the faction xml and adding the following.
The first 3 numbers are those you get from the colour picker in the order they are displayed.