Programming Atmel SAM MCU using SAM-BA
Something I noticed is that you have the following line to toggle the state:

ioport_toggle_pin_level(IOPORT_CREATE_PIN(PIOA,14));


While technically there's nothing wrong with that most Atmel examples define the port in conf_board.h so if you haven't changed that you've probably also missed configuring the port as an output. Try adding the following to configure the port as an output and it's probably a better practice to define the port name in a define:

#define LED IOPORT_CREATE_PIN(PIOA,14)
ioport_set_pin_dir(LED, IOPORT_DIR_OUTPUT);


Then in your main code:

ioport_toggle_pin_level(LED);


Regardless of whether that works on not it's worth taking a look through some of the ASF generated code in the subdirectories of the project to become familiar with where Atmel normally place the port configuration and initialisation code. There may be other pins being defined as outputs that your board doesn't like. I couldn't find a schematic for the Arduino Due but it might also be worth finding out what crystal frequency it uses, it may be different enough that the clock initialisation code selects a frequency that is too high to work.