I ran into this same issue. I could not find a way around it. Just always leave your Gamepad plugged in?
You can tell windows which joystick to "prefer". Then programs which, by default, only use "joy1" will instead use whatever joystick you have set up as the preferred stick. It doesn't allow you to tell windows which one should be "joy1" or "joy2" or "joy3" though.
To do this, go into the gamepad settings in the control panels. I believe its in the properties there somewhere.