Maybe the AFCAD file that is installed do not have the same altitude defined, as inside the visual model: the scenery.
If you install sceneries, check the AFCAD file before so it was matched with the scenery. Use always the desired AFCAD file with the proper scenery. Many AFCAD file creator make files for default airports as well. They are good too. For example I use default Heathrow scenery, with an edited AFCAD, but I have some add-on airports, which I had to download proper AFCAD files for.