This is a bug I used to see in WOM too. Every so often the game will swap the colors of all the kingdom/empire borders around. Altar was red, and is still listed as red in the Faction Power screen, but suddenly the borders to their realm are yellow. My custom kingdom was dark red, now they're light blue. Gilden was yellow, now orange. Etc.
Here's a save game with the issue. It occurs on reload, quitting and relaunching EFE, whatever. Once they swap, they're swapped.
