It's not very clear which airplane you use, if it's internally supported by GSX, or if you customized, or you made a custom config from scratch. Passengers in the air can be caused by either of these:
- A wrong airplane configuration, with doors not set correctly. This is fixed by correcting the airplane configuration and set all the doors in their proper place.
OR
- A scenery you have installed (usually from OrbX) that has changed the default ground elevation. This is fixed by using the GSX parking customization page, and clicking the small airplane icon on the top right of the window, where it says "Airport Elevation"