The installer doesn't do anything wrong with your scenery.cfg.
If you are seeing an error now, it's because the scenery.cfg already had an error before installing the scenery, which are always caused by trying editing it by hand.
When you hand edit the scenery.cfg and put an error in it, FSX will tolerate it, so you might not notice, but any installer that obviously use standard Windows function to modify .INI files (the scenery.cfg IS an .ini file), will probably be confused by the error that was already there.
the Area and Layer numbers now different ! this is not ok
If there are no other errors and your sceneries works fine, non-matching Area numbers and layer numbers are NOT A PROBLEM.
The whole point of having a separate Area and Layer number is to allow to change the priority of a scenery (the Layer) without changing the order in the file (the Area), otherwise why the need to have an Area and a Layer as separate commands ? They ARE supposed to be possibly non-matching, it's all normal.
Of course, assuming everything works normally and you don't have other problems related to the Scenery Library, which seems to be the case reading your message.
