Why does my LED turn off automatically after about 18 seconds on its own?
Again, figured this out. I simply forgot to put in board_init(); Also, since board_init() already calls ioport_init(), I had to disable that.

Now I have this:

int main (void)
{
    /* Initialize the SAM system. */
    sysclk_init(); // Initialize the System Clock
    board_init();  // Initialize the board


....