UPDATE - think I've found the solution so if anyone has the same issue here's how to fix it:
In your supermodel.ini look for the line: InputAnalogJoyX = "JOY_XAXIS_INV,MOUSE_XAXIS" ; analog, full X axis
Change this line in include the _INV command which will invert the direction:
InputAnalogJoyX = "JOY_XAXIS_INV,MOUSE_XAXIS_INV" ; analog, full X axis