Arduino Nano V 3.0 usb fails if Vin powered

I chose the Nano to be embedded in a pcb, but I notice in testing that when the device is powered via Vin (12V), when the usb connector is plugged in, Windows complains that the port does not work. This is annoying as it means an extra jumper in the pcb to disconnect power if the usb connect is ever needed. Anyone else come across this or am I doing something stupid?