Those messages indicate that the J-link adapter is just not seeing any sensible data on the JTAG pins. Assuming that your hardware is working correctly, then the JTAG pins may not be mapped to JTAG depending on what software is loaded in the SAM3X, a whole chip ERASE should clear that. Another thing that could cause this is a misconnected header. It is worth noting here that the orientation of the JTAG header on the Taiji is 180° opposite to the Due, which could lead to confusion. There is a small dot on the board indicating pin 1, easy to miss.