Architecture: SAM
Board: Arduino Due
When the pin is defined as OUTPUT it automatically sets HIGH in that pin, even when digitalWrite previously set it LOW. This is different behavior from AVR.

I need all DO set low at startup, so in Arduino/hardware/arduino/sam/cores/arduino/wiring_digital.c. To make pinMode output LOW by default, change PIO_OUTPUT_1 to PIO_OUTPUT_0.

See http://forum.arduino.cc/index.php?topic=185230.0 and http://forum.arduino.cc/index.php?topic=154869.0