I worked on a very low power application some years back. The microcontroller (sorry it was a PIC) did the power down thing and was able to achieve an idle current of 2 uA. In order to get the current this low I had to force all I/O pins as outputs and to the logic state near GND. You discovered the same thing I did, that any pin to the microcontroller that is an input or high output sources current, albeit at leakage levels, into any other attached circuitry.

I also had to design the device with a power switching circuit to cut off power to all other circuits when in the standby mode. It turned out that in order to get lowest possible current I used a relay to cut power. The other circuitry external to the microcontroller included an RF transmitter and required a high operating current. There was too much leakage through a power transistor to use it as an effective power switch. (At the time cost effective MOSFETs with low gate drive voltages just were not available).

Michael Karas