This causes the uncontrollable scrolling effect when starting up the game. It also assumes the axes do different things or are in different positions.
The game assumes there's an Xbox 360 controller, which has more than four axes. After spending an hour experimenting with it, I figured out how to make it work. I purchased Saints Row 2 off Steam only to discover my PlayStation DualShock controller doesn't work out-of-the-box with it.