This might also happen if you use an add-on product that changes the Scenery Library, like a scenery.cfg manager, or some of the ATC products that creates AFCADs on the fly.
But, it might also happen if you have a corrupted .BGL somewhere. If you enable logging in the Troubleshooting section of the GSX Settings menu, and have a look at the Couatl.LOG file that will be produced, it will tell you if corrupted .BGLs were found.