My game doesn't seem to have any option regarding the spawning of self-created empires. Where is that "Empire Spawning Disable" option you talk about?
When starting a new game, the empire selection screen on the left corner of the screen will show the available pre-generated empire, with any player created empires sorted at the top. Each player empire has a little button to the right shaped like a bird that toggles various spawning options (forbidden, allowed, and forced).
I've noticed that some people are unable to see this- my guess if the set resolution is too small the interface is cut off.