It happens the same to me, when using the programming port with the Arduino Due, I can only connect to the Native USB.That would be logical. The programming port is for, well, programming the Arduino. You aren't programming the Arduino from the Terminal application, are you?
I am not, but wouldn't I be able to communicate to Arduino Uno via Serial.print() and Serial.read() commands?
I don't understand why the port is not available when I try to open it from another program different from Serial Monitor (which is supposed to be the same).