Is your GPS hooked up to the CanBus connected plug of a recent BMW bike?
I think as part of its shutdown sequence, the CanBus becomes active for a brief period some moments after the ignition is turned of, and this event might be confusing your GPS and causing it to wake up again.
The easiest solution might be to simply bypass the CanBus and hook up your GPS directly to the battery using a fused cable (and maybe a relay).
This is just a hypothesis, I have no idea why the CanBus would become active again... perhaps part of the immobilizer logic or alarm being activated. I'm looking into my own wiring options and have read others having similar problems as yours.