1. It does halt windows from shutting down and impose its own timer to allow you to select the shutdown option. It should execute the default shutdown option after the timeout. Is this not the case? Do you have a shutdown option set to hibernate in shutdown settings?
2. What happens if you zoom out then zoom in? This will reset the GPS position in StreetDeck. If that doesn't fix the problem, its more then likely your hardware, if it does fix it, let me know. Also, what happens if you goto the navigation settings, select a different COM port, hit save go back, select the correct COM port hit save then go back to navigation. This will reset the GPS itself to the extent its possible to reset a GPS.