Do I have to plug out wires from 3V and GND pins when I upload a sketch into due

I have udoo board and it contains arduino due board. When I use external computer to upload a sketch to it, my program does not find the board. But when I take out wires from GND and 5V/3.3V pins, the program finds the board and it uploads the sketch as normal. Is it really normal process for arduino due, or the board is damaged? Thanks