Hey jtslade,
In the Windows' game controllers panel, I have the "Pedals reported as...Combined (single axis - used for most games)" unchecked.
In the emulator, I have the Accelerate and Brake Invert option checked. In addition, I chose the G25 Accelerator to be the Accelerate and the G25 brake to be the Brake, from the drop-down option (when you double-click the control option).
I haven't experienced any problems thus far.
Hope this helps you.