I'm actually having the same problem, and I'm using the wired 360 controller. I can map SOME of the buttons, but it doesn't matter as nothing on the controller works in the game :\
If you are using the 360 controller, you don't need to map any buttons. Unless you want a custom control layout. And, you would do that in game, not in some external program. Some controls may not remap, like the Joysticks, but all the buttons should.
Interesting, guess I'll hold off on running out and buying a 25 dollar controller like the Mod suggested............
Good, because the $25 controller won't work. The one that does work costs $40
http://www.amazon.com/Xbox-360-Controller/dp/B000B6MLTQ