SAM3/4: Fix GPIO pull-up/down code.

Enabling the pull-down resistor while the pull-up resistor is still enabled
is not possible. In this case, the write of PIO_PPDER for the relevant I/O
line is discarded. Likewise, enabling the pull-up resistor while the
pull-down resistor is still enabled is not possible. In this case, the
write of PIO_PUER for the relevant I/O line is discarded.