Regardless the cause of that issue, you should be able to simply download the entire game if you have a fast internet connection--all you need is your serial key. Here's how:
1) Download and install
Stardock Central.
2) Log into SDC with the same details as you did on the forum here.
3) In SDC, Go to the tools menu and choose Register Products.
4) Choose 'Games' at the left side of the registration dialog, then in the drop-down list on the right, find and select Galactic Civilizations II.
5) Input the same email address you used for your forum account in the appropriate box, as well as your serial key in its box.
IMPORTANT: The serial key you must use should be 28 characters long and contain only 0-9 and A-F, with NO dashes. If you have a serial that begins with 'GC2-' and contains dashes, look through the packaging for a second one. The 'GC2-' serial will NOT work for registering the game, so don't try to force it--if that is the only serial your game came with, post back here again for further directions.
6) Once you have filled in those details, click 'Register'. A message should pop up indicating success or failure (if it fails, post back here with the exact message it gives). If it succeeded, you can then close the registration dialog.
7) Back at the main screen of SDC, go to the network menu and choose Games.
8) You should be presented with a list of SD-published games. At the top of the list, there should be a 'Purchased Products' heading, with GC2 listed right under it. Just select GC2 and click the Install button that appears at the right, and wait for it to download (you may also need to click the [+] next to GC2 and install the extra components as well if you are not automatically prompted to install them with the main GC2 itself).