Good luck. I stopped playing (well, never even started really) because of this issue. I use the wired 360 controller straight from MS and it's a completely buggy POS. The game was not meant to ever be played on PC IMO, which is why I think it was being sold for $1.99. They knew they'd recoup some losses of making such a shitty port.
Anyways, I have a similar issue. For me, I see the button mapping the same as you do (Button 1, Button2, etc). I found that the only way to get the controller to even remotely work was to start the game and not touch the keyboard or mouse whatsoever after that. I have to do everything through the controller. Unfortunately, because the button mapping is so fucked, I have no idea what does what...and to be quite honest, it's too much of a waste of my time to have to figure it out.
If these losers can't program a controller to work and map correctly, I can only imagine what a waste of time the shitty gameplay will be.