this is probably a bug in the SPI library.
May you try to change the file:
hardware/arduino/sam/variants/arduino_due_x/variant.h
and replace the following (should be around line 87):
#define BOARD_SPI_DEFAULT_SS BOARD_SPI_SS2
with:
#define BOARD_SPI_DEFAULT_SS BOARD_SPI_SS3
and see if this solve your problem?