Did you set them to be inverted? I had to invert the vertical axsises I think to make them work the way I wanted? Look at the axis menu, there should be an inverted axis submenu
I did not see an option for inverting them to make it work correctly.
I am having this issue as well. My Saitek P990 USB Controller is not detected by the game at all no matter if I have it plugged in before starting the game, also updated drivers as well. The game simply detects nothing but the keyboard.