When you switch worlds, the colors don't update. So if there is a biome with ID 30 that's blue on world 1 and you switch to world 2, where biome 30 is red, then the biome will still look blue.

Originally reported by IRSmoh:

http://dev.bukkit.org/server-mods/terrain-control/forum/39789-new-versions/?page=16#p323