This has been a known issue since the beginning of time for pc users using an xbox controller to play FFXI.
"The bumper buttons cannot easily be assigned the same button settings as on ps2 or xbox360 while on a pc".
The game or the way that microsoft has made their adapter for xbox360 controllers, to my understanding, see the bumpers as a coordinate plane rather than buttons... (like a joystick would be).
I would love to be able to use the bumpers while on pc. Is there any way, through SE, or additional patches for the product that this can be achieved?