I don't know if this is meant to happen or what. But when I started playing dark avatar on the custom mode (this never happened when playing dreadlords) almost all the starting space miner, colony and flag ships for all the major races start in the same corner of the map. Then 2 races have their starting ships randomly next to a planet somewhere else.
I'm not sure what i'm doing wrong because I have gotten the starting ships to be next to their starting planet before a few times.