Input Focus
From Unofficial TransGaming Wiki
Some games or applications may suffer issues where they do not have keyboard and/or mouse focus. This will prevent the application from receiving input from the keyboard and/or mouse respectively.
Such issues may vary depending on window manager used and on options selected. It is worth experimenting with these settings to see if you can fix the problem.
An effective but difficult to implement kill-all for these issues is the use of a second X Server.
Relevant Options
Managed: Controls whether your Window Manager\Desktop Environment is controls the drawing of windows.
DXGrab: Enables or disables a DirectInput function call that permits applications to obtain total control of the mouse.
Desktop: Instead of starting the game on your desktop, creates a virtual desktop with a specified resolution in a window on your desktop.

