Did you download both the Phantom 2 Vision+ Assistant Software v3.6 and Phantom RC Assistant Software v1.2?
You need them both to do all the calibrations and any updates to the Phantom and the transmitter.
Plug it in to the computer by usb. turn on your controller. Then open RC asst. 1.2. You should hear the connection tone when you connect to the computer when you turn on the controller.