The new SDC build has a new activate.exe in it which will hopefully allow you to activate GC2 without any further problems. If you have a firewall, please allow activate.exe full access, or turn it off completely while trying to install, update, or activate GalCiv2. Please make sure that you are using the California server.
To set SDC to use the California server, go to Tools->Settings->Internet.
If you still have problems, please send an e-mail to kwilas@stardock.com with your name and e-mail address that you created your Stardock.net account, and tell him what operating system you are using, if you have any firewalls, and what kind of internet connection you have. Also please give him any error codes that you may have received.