I've installed the 05 over my .00 version, but every time I shut off my computer, turn it back on, and play the game, it says on the main menu it's version 1.00.00. Do I have to keep re-installing it?

You should not have to keep reinstalling the game to update the version. It sounds like the installation program is not being allowed to overwrite the files in the game's application folder. Are you installing the update from an account with administrator privileges?

Yes, I am.

As long as the 1.00 version and the 1.00.05 version both came from the same game site, there should be no reason that the update would not overwrite the game's files. However, there are some things you can try. First, back up your savegame files using the procedure in this post, so that you don't lose your game progress in case something goes wrong. You should not need to restore the savegame files, since the uninstall program doesn't remove them, but they are preserved in case you need them. Then completely uninstall 1.00 and run the setup program for 1.00.05. That should resolve the problem.