The first game I tried was fine, but in my current game...
All sorts of problems with starbases. Two resources are within 4 squares of each other (there's three squares between them), but I could only colonize one of them. The other gives the message about being too close. This shouldn't happen, regardless of how close they are.
I destroyed the first starbase, then built on the second resource successfully. Shortly thereafter, my starbase was wiped out. I was then unable to build on either resource (kept getting the error message). There were no other starbases nearby.
In this same game, I was unable to mine any resource (the resource acted like a normal starbase). Additionally, clicking on a resource starbase resulted in the message "harvesting this resource will give you a great advantage" or some such, rather than the starbase inventory screen.
Lastly, the "starbases are too close" error message continues to pop up at random intervals, regardless of what I'm doing (i.e., even when there's no constructors anywhere near a resource!)
My guess is, something I did early on in this game triggered a whole series of bugs. Frogboy, I'll keep the savegame around if you wish to look at it.
Foul
P.S. I'm not real big on the expanding minors, either. In my opinion, it makes the initial game harder -- you're competing with not five, but eight other expanding empires. Maybe set the minors on a timer, and let them expand after a certain number of turns?
P.P.S. While on the subject of starbases -- I artificially limit myself to a maximum of two starbases per sector. This makes "Painful" only beatable (by me) about 50% of the time, and higher levels are fairly impossible. Which is about the way it should be. I'm guessing that 90% of the Metaverse leader board uses such "exploits" (as I consider them) as culture bombing, production bombing, etc to win. Limiting these exploits/features further would put the players on more even keel with the computer, who never builds 32 starbases in a sector.
~SDC~