If you're certain it's in the right location & properly installed & activated check the altitude of your airport in FSSC with the actual altitude in FS9. The scenery objects could be underground which is why they don't display.
One of the features I like in FSSC is the Area16N flat area. You can use this to level various parts of the mesh surrounding your airport to any altitude you wish. This saves messing around with manual Flatten switches in Scenery.cfg. If you use this for your existing scenery you will probably have to change what you did previously in AFCAD.