There is a bug in Ubuntu/Unity (Ubuntu's window manager) that means the launcher and title bars do not disappear when you are in a fullscreen game that does not support your native resolution: https://bugs.launchpad.net/ubuntu/+source/unity/+b...
Emulate a Virtual Desktop (Graphics tab) This makes any programs in the bottle display at a certain size. The effect is that a program will think that it's running full-screen, but it's actually running in a window on your desktop. This helps alleviate window management problems in some programs. Click on Emulate a virtual desktop and set the desired size. Stick to a 4:3 aspect ratio like 800x600 or 1024x768.
I tick "Emulate a virtual desktop" and use the size 1280x1024, which is the maximum resolution supported by AOE II.
In the game, go into Options on the main screen and under Screen Size, select 1280x1024.
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