The problem you have is that the analog triggers register as additional axis, not buttons. For games that officially support the 360 controller for Windows (many newer ones do, FFXI does not), the controller works exactly like it would in the 360 version of the game. When the controller isn't directly supported, however, you run into what you have - that the triggers don't act as buttons. For that you need to use third party drivers for it.
XBCD would be the common one.