starbase question

I just played a game where 2 different resources were in the same sector as 4 of my planets. I built starbases at both resources. When upgrading 1 base for production, I got no benefit as the other base already had production benefits. It was easy to tell as my planet was class 40 and had all manufacturing projects, including Omega and Hyperion powerplants. What does the code do when there are 2 or more starbases in the same sector? Where do I put my upgrades?