The most likely explanation is: when you parked manually using the visual scenery as a reference, but you might have ended outside the parking radius, perhaps because the center and radius in the scenery AFCAD are not set correctly in relationship with the visual scenery.
Instead, when you select to start a flight using the FSX Go To menu or even the GSX Warp to option, it will always place exactly in the center of the parking radius, so it will always registered as a parked position, regardless of the visual scenery outside.