It sounds like you have a bad install cd. If you have a fast internet connection, you can simply download the entire game instead. Here's how:
1) Download and install
Stardock Central.
2) Log in on SDC with the same account you used on the forum here.
3) Go to the Tools menu in SDC, and choose Register Products.
4) In the registration dialog, click 'Games' on the left.
5) Find Galactic Civlizations II in the 'Product' pulldown menu on the right.
6) Enter your email address (same one from your forum account that you logged into SDC with) and your GC2:Gold serial number, and click 'Register'. Find Dark Avatar in the Product pulldown and do the same for it (just to be sure).
7) Close the registration dialog. Back on the main SDC screen, pick Games on the left, and you should see Galactic Civlisations II listed under a 'purchased products' heading. Simply select it and click the Install button that appears next to it. If you aren't prompted to install the modules as well (Tutorials, Movies, Multimedia, and Dark Avatar), click the [+] next to GC2 and install them as well.
Then just wait for the game to download. That's all there is to it!