I actually took qrtxian's word, and modified my files so there are only 4 influence modules available, all on the diplomacy branch, except for the race-specific ones (Krynn and Thalan). I made them powerful and expensive, and also made the techs expensive. They're balanced because they're very powerful, but fully upgrading a starbase will cost you close to 2000bc.
I've made many test-plays today and I've seen games with no influence starbases at all, games with plenty but not upgraded, and games with a few ones upgraded. It seems very random. I made these tests by using the CTRL+Z cheat and watching the AIs develop.
I'll look at your starbase XML MarvinKosh, maybe I'll learn something. Although your mod changes the techtrees so drastically that the behavior you describe might be attributed to something else, rather than the StarbaseModules.xml.
EDIT: Your StarbaseModules.xml looks pretty vanilla, except for the inverse order you mentioned. I'll try that.
EDIT2: Also, playing with CTRL+Z isn't the most reliable method of testing, since the AIs have little time between turns to think ahead, and sometimes the AIs seem to go full retard. But I don't really have the time and patience required...