I see, so basically it's not seeing that you have the X, Y, RX, and RY axes setup. It uses a simple axis exist check to make sure they are their before mapping them, maybe something is interrupting the results. Do you have PPJoy installed?
EDIT: I also meant to mention that I will be adding manual joystick axis assignments.
After configuring vJoy?
No I dont have PPJoy installed, perhaps there is another program that its conflicting with...