Welcome to the forums.
I just did some testing with Gold and I couldn't select multiple planet starts for the same player either.
It ignored any extra start planets and just built new planets in the same home system as the first assigned planet - strange...
I thought Gold would have looked at this issue.
One PBW Game I hosted (Pre-Gold), I used this to my advantage. You assign a Huge World as the Starting planet, and then in the game setup, select 3 Home Planets with 'Average' value. In effect this gives you the Huge World you assigned and 2 Medium Home Worlds, all in the same system.
Starting planets seems to take the largest planet in any given sector for the Home World, so it shouldn't assign a moon as the Home World.