The stock scenery included with Prepar3D v5.3 is a lot bigger and features a more recent airport and navigation data set, including radio comms, approaches, runways, parking locations etc.
Since the parking locations in v5.3 may have changed at the airport you are currently located at from v5.2, the aircraft might not be located at a parking spot.
So before building a new flight, please choose a listed parking location for your aircraft on the Flight Generator page so that the aircraft is properly located in a start position taken from the new data.