Check gameplay.constants?

I've had this issue before, though it involved giving the pirates a second and different starbase

there is a research point for changing the max training level for each race, I think when you made a second seperate one, even though it was different it went haywire

Well Sins errors are like hardcodes, they aren't always ment to make sense, but only to be known. I once had an error where i would get a minidumb everytime I hovered the curser over a research picture in the research tree. It showed out to be because I had set the logistics page and tactical page in the player*.race to 0 (this race don't have any modules). The error was gone after adding some modules to each page.