From: Ol' Blighty
I can't help Mozo but I know what is causing your problem Sabre, as soon as you say you got it when you installed mods.
When you started a previous game did you add AI Empires manually at all? If so, any races that are not available in the mod, for example, the default races may not be available in the Trek mod, but the Galaxy setup has remembered you choosing that no longer existant race, so the box will appear for every single AI Empire you added manually. Before you change themes, remove any manually added Empires from this screen.
Another similar error can happen with incorrect file structure setup for mods.
"My body may be confined to this chair, but my mind is free to explore the universe" - Stephen Hawking