I am an un-armed transport commander. So I don't leave my CC anywhere. Go down to a planet surface, order my SC to deploy mining drones, go to another base to sell what I have, go back recover mining drones and repeat.
What I had to do was uninstall BCMG, delete the entire 3000AD directory, reinstall, move the patch exe's to the Battlecruiser Millennium Gold directory, then run the patch exe's. Both patches worked fine for me.