There is a sticky thread in this section titled "Tweaks Thread". If you have looked in there, you might have seen that in it is a tip on how to map the shoulder buttons as the mouse-buttons. You may be able to apply the same guide to the gaming buttons.
I do not know if this will affect other software, but since I seem to recall that the shoulder button remapping can cause problems, I would imagine that you would get the same results out of the game buttons, too.