So please tell me I am doing something very wrong and that it is an easy fix.
Use this app:
http://www.generalarcade.com/gamepadtool/It outputs the assigned buttons formatted as below:
a:b0,b:b1,back:b9,dpdown:b12,dpleft:b13,dpright:b14,dpup:b11,guide:b10,leftshoulder:b4,leftstick:b6,lefttrigger:a2,leftx:a0,lefty:a1,rightshoulder:b5,rightstick:b7,righttrigger:a5,rightx:a3,righty:a4,start:b8,x:b2,y:b3
You should then be able to make a config using the following:
b0 = Button0, b1=Button1 etc
dpdown=digital pad down etc
Good Luck!