I found
this bit of information over on the Sprint forums on the matter.
It's still a bit speculative, but the suggestion is that using the kill switch doesn't allow the ECU to follow its normal shutdown procedure before turning off its own power.
You can hear this process when you turn off the ignition with the key - a relay clicks under the seat about 5 seconds later when the ECU has finished committing data and cuts its own power, so it should be easy to tell if this is not the case when using the killswitch.
I'd be interested to see a wiring diagram, but it sounds feasible.
The question is, what problems are caused by giving the ECU a dirty shutdown, and how can these problems be resolved? Probably a dealer or a TuneBoy!