First, you must be sure that's another scenery for the same airport is not taking precedence. And, it's possible that, if that AFCAD has errors, GSX will discard it. It will also discard it, if it's not self-contained, meaning it requires data from another (usually the default) AFCAD.
You might have better informations about the problem by enabling Logging in the Troubleshooting section of the GSX Settings menu. Go to that airport, then exit from the sim. The Couatl.LOG file that will be generated might have some infos on why the AFCAD hasn't been used.