Then your scenery.cfg was ALREADY corrupted before you installed JFK, but in that case, you should have seen an error message from the installer, that your scenery.cfg was already corrupted before starting it.
A corrupted scenery.cfg can only happen by having edited manually OR by running a bugged installer from other products, but is very quite unlikely.
If the installer found a corrupted scenery.cfg (and, as I've said, it would ALERT you of this) it would abort and not copy any files so, you won't see any scenery.