In the game you probably have the pedals inverted. Goto the OPTIONS > CONTROLS menu, and click on the Axes/FF button. There you should see the Axes for the pedals assigned to Throttle and Brake. You can choose to Invert the brake pedal.
You may also want to have "Seperate Pedals" turned on in the game. But also make sure that Combined Axis is OFF in the Windows Contoller Options.