In the manual for the IC-746, the remote port is identified incorrectly. The image from the manual identifies the Remote port as the Speaker Port and the Speaker port as the Remote port. 
If the USB-RTS01 cable is connected to this port, communications will not be possible from the radio to the programmer or to any other remote-control software. This just is not the right port.
Shown here is the cable connected correctly to the back of the radio. 