If you can upload a sketch (Blink sketch from the example sketches) and the sketch runs properly when connected to the Native USB port but not when connected to the USB Programming Port, IMO there is a good chance that the Atmel 16U2 on the board has not been programmed properly by the board manufacturer.
Ask a refund to the board reseller. BTW, this is not a frequent issue with clone boards.
FYI, if you want to upload a correct program in the Atmel 16U2, follow these tutorials:https://www.arduino.cc/en/Hacking/Upgrading16U2Duehttps://www.arduino.cc/en/Tutorial/ArduinoISP
Plus, add logic level shifters between, for example an UNO as ISP (5V compliant), and the DUE (3.3V compliant).