Problem with DUE during power up

I have the problem with DUE similar to the posts below:

http://forum.arduino.cc/index.php?topic=197205.0
http://forum.arduino.cc/index.php?topic=194913.0
http://forum.arduino.cc/index.php?topic=194782.0
http://forum.arduino.cc/index.php?topic=200854.0

Those may not be all post that I can dug out. The problem happen when using power either though USB or DC Jack. The code (sketch) refuse to start. However, when using serial monitor the code running just fine.

I read torwan's post (DUE doesn't start properly after applying input voltage (dc/usb), have to reset - Arduino Due - Arduino Forum). He got a workaround solution. Could you be kind to share with us here? So I know where I should start to modify the firmware for ATmega16U2.