Hi Atul,
In general a particular MCU may have port pins that are included as part of the MCU but are not brought out to a physical pin on the part. These are called unbonded signals, and need to be addressed when you are in low power modes. Make sure that all unused Parallel Input/Output signals are set to a known state, such as output driven low. If you do not initialize all the ports on an MCU, then they typically default to inputs that are not pulled up (FLOATING INPUTS !!) I have seen these floating inputs consume ~150uA each in Stop modes on 9S08 MCUs.
Enough for theory. Initialize ALL your ports pins to outputs and set them low, unless you are using them for something specific. Figure 1-7 in the MC1321x Reference Manual v1.1 has a few clues for you listed as Notes 1 & 3. I would check to make sure PortF and PortG pins are set to outputs driven low, if possible.
Hopefully this will help clear up some of the current measurement problems. Also remove the BDM when testing. Measure Idd as close to the MCU as possible to ensure you are measuring the current going into the MC1321x only, and not peripheral components on your board. The LVI adder is 70uA, so you may want to disable it too.
Measuring current is the best way to make sure the MCU is operating in the correct Stop mode, keep going with section 6.3.2 of the MC1321x data sheet!!!!
Thanks,
Rick