[raynor]

Before you start the game, go to each race you added and switch it to computer control as well as telling it to use the Race Style ministers. After you've already started a game, you need to go to Empire Options->Ministers and click 'Complete AI On' before you switch it to human control.

The game sorta randomly picks the mod races with the rest. But, painful though it may be, you're a lot better off just adding them yourself and manually switching them to computer control/use Race Ministers.