In case it is of use to anyone, if you need to change the pullup/pulldown configuration of the GPIO you are configuring in init.d then you will need to use this:
raspi-gpio set 17 pu
example is for gpio 17
This is an an alternative to writing something to /sys/class/gpio/gpio17 which doesn't appear to support pull/pullup/pulldown
I would have put this on the init.d page linked above but there is not facility to add comments there