If you have add-on like ORBX or some other mesh that might change the elevation, that could be it. There are two ways to solve this. If you have ORBX Vectors, you can run the AEC to fix the elevation issue. If you do not, when you load a flight, go into the GSX airport customization, at the top right corner, there is a button with an airplane icon on it. Click on it, then save changes. This would have to be done at every airport that has this issue.
