Completely install the main game and the three expansions before playing and/or registering any of them. The expansions contain key files that will alter the original game and complete its installation. Once all the games and expansions are installed, the registration keys will work properly.
Here is a guide on how to install the bundle:
If you have an older purchase for only the main CIV IV game, you can obtain a patcher, here, that will fix the issue: