do you have to run games windowed with desktop running for any particular reason? If no then try giving your games full control of the mouse and see if that works.
edit ~/.xinitrc and # out any existing uncommented lines then add
Code:
exec *path/to/game/executable*
finally telinit to a cli runlevel so lets try
(you may need to switch console using ctrl+alt+F1 to F8) and run
Now you may beed to be root to do some of this but remember NEVER EVER EVER run the X server as root.
If all works fine then you will know that it's just your DE not the native games. FYI never run ram and virtual memory hoggers for graphics such as games because they eat system resources and makes your games slow and even LAG.
If the above did not work then perhaps it's to do with how you set up your mouse.