If you bought a CD copy of Age of Empires 3, you will have a prompt box on launch asking for a CD key. It was not working correctly for me, and I can show how I fixed it.
The box should have have 5 smaller boxes each holding 5 characters. This allows for a 25 digit code. However, when I first tried launching the game, some boxes were only holding 4 characters, rendering me unable to enter the code. The solution for my case was to install "Core Fonts" into the bottle, which allowed my to enter the CD key properly.