You need to look at your scenery.cfg file DIRECTLY.
Find it (in your main FS9 folder) and right-click on it. Use the Open With option and select Notepad.
Now, you can read (write and edit) your CFG file without using the sim's clunky scenery manager.
You'll see a bunch of add-on "calls" that look like this:
[Area.041]
Title=MAIW Land Class
Local=Addon Scenery\MAIW Land Class
Remote=
Active=TRUE
Required=FALSE
Layer=
41
[Area.042]
Title=Static Objects Library
Local=Addon Scenery\Static Objects Library
Remote=
Active=TRUE
Required=FALSE
Layer=
42
[Area.043]
Title=MAIW Scenery Library Objects
Local=Addon Scenery\MAIW Scenery Library Objects
Remote=
Active=TRUE
Required=FALSE
Layer=
43
Pay attention to those "Layer=" lines, that's where your mystery land-fill is causing problems (usually).
Note that my Area and Layer numbers match and are in order. That's what happens when you manually add and edit scenery layers.

Those Layer= lines can look a little like a dumpster fire if you use the scenery manager.
I would guess that your scenery has an added Land Class file that's causing issues.
