This prolly ought to have been posted over on the Galactic forum; however, I had a similar problem. I had downloaded the game, then tried to update it via SDC. For whatever reason this didn't work very well at first, so I then downloaded the entire bonus pack and tried to install it that way. Finally, though, when the first patch/update came out, I went back to SDC and tried to get it. Through that process, I realized that my registration hadn't taken, so I had to put my serial number back in.. to do that go to the Drengin.net tab, right click on it, choose "account" and fill in the serial number box if it is empty.. when I did that, I saw that the bonus pack came up as available.. even though I had downloaded it, it still hadn't really installed! So I updated everything again (very short process even on 56k) and this time everything took. The difference in the game is remarkable, btw. You need to get the bonus pack.
I hope some of this is helpful to you; if not, keep looking for the reasons.. could be that you need to go to the tools menu and "refresh" .. try both of these methods and see if any of it works for you.
Stardock Forums