Hi Zeb:
Possibly you have some "excludes" in the areas where your scenery objects are placed ...which prevent the scenery library objects from being displayed in FS ?
[
EDITED]
After making sure that there are no "excludes" in the areas where your scenery objects are placed ...which prevent the scenery library objects from being displayed in FS, one would next analyze what is going on with the scenery object placement BGL(s).
After analyzing what is going on with the scenery object placement BGL(s), one would next analyze what is going on with the scenery object library BGL(s).
As you may know, typically 3D scenery object MDLs are packaged
without placement info inside a compiled BGL, referred to as a "scenery object
library" BGL
.
And one would typically "place" those 3D scenery objects in FS via
IS3 by writing the Geographic coordinates / Heading / Altitude / Scale info ...inside another type of compiled BGL, referred to as a "scenery object
placement" BGL.
When we "place" those 3D scenery
library objects in FS by writing pertinent info into a "
placement" BGL via IS3, we must right-click the ground to begin the "
Save process" via:
IS3 right-click context menu
> Add To File... ( [Save As] dialog pop up)
...and we are then prompted for the name of a BGL into which we intend to save the current selected object's "placement" info.
By
default,
IS3 proposes the name "
InstantScenery.BGL" for one's first "placement" BGL used to save such "placement" info
.
That
default name "
InstantScenery.BGL" will be submitted in:
IS3 right-click context menu
> Add To File... [Save As] dialog > {
File name} field
In the same dialog box, by
default,
IS3 also proposes to save "
InstantScenery.BGL" ...into
this folder location path:
[FS install path]\Addon Scenery\Scenery
FYI: By default IS3 picks that name and folder location path because
[FS install path]\Addon Scenery\Scenery is always set "active" in the FS scenery library GUI (...and the linked Scenery.Cfg file).
We can also choose a
different pre-existing or newly created file name, and we can choose a
different pre-existing folder location path ...into which to save our "placement" info for the current selected object.
By default, IS3 'remembers' the name of the "placement" BGL file name
and its folder path location we
last used to save such "placement" info
; that name will be submitted in:
IS3 right-click context menu > Add To File... > [Save As] dialog
> {File name} field
Thus,
IS3 remembers either the
default "InstantScenery.BGL" file name and path
, or any
"custom" file name and path ...for the
last "placement" BGL we used to save such "placement" info.
IS3 also allows us to "
Open" only
one pre-existing "placement" BGL at a time to Add / Edit object properties / Move / Delete ...its scenery library object "placement" info.
CAVEAT: When we exit FS, then re-start FS, by default,
IS3 does NOT automatically reload and allow display of objects we have previously placed via IS3 ...as long as IS3 is "managing" those objects.
If we wish to allow display of objects we have previously placed via IS3, (...
each and every time we re-start FS) we must:
1.) Manually launch
IS3, then:
a.) "Open"
each pre-existing "placement" BGL which is used to "place" objects at the flight locations in which we will be viewing scenery within our user aircraft
NOTE: Those pre-existing "placement" BGLs must be manually loaded
one at a time; after each is loaded, they all stay "
active"
during that FS session
, but will NOT stay "active" after exiting FS.
Inconvenient ? ...YES ! 
...But there is a work-around for this. 
After
completely finished working with a "placement" BGL to Add / Edit
(object properties) / Move / Delete ...its scenery library object "placement" info,
move it to a new folder path so that
IS3 no longer knows its location, thus preventing IS3 from exerting continued "control" over object display for
all objects placed via that "placement" BGL.
This effectively transfers "management" for the display of all objects "placed" via that BGL ...
back to FS.
CAVEAT: If you once more "
Open" such a pre-existing "placement" BGL to Add / Edit object properties / Move / Delete for any scenery library object's "placement" info, and save any such changes to that BGL manually via the IS3 GUI,
IS3 "
knows-where-it-lives"
again, and will resume taking exclusive "control" over object display for all objects placed via that "placement" BGL.
So, once again, one will be subject to this "inconvenient truth" about working with
IS3:
When we exit FS, then re-start FS, by default,
IS3 does NOT automatically reload and allow display of objects we have previously placed via IS3 ...as long as IS3 is "managing" those objects.
...And once again, we will be compelled to use our "work-around" for this:
After
completely finished working with a "placement" BGL to Add / Edit
(object properties) / Move / Delete ...scenery library object "placement" info,
move it to a new folder path so that IS3
no longer knows its location, thus preventing IS3 from exerting continued "control" over object display for
all objects placed via that "placement" BGL.
Hope this helps sort out the scenario you are troubleshooting; if you still have any ongoing issues after implementing the example "work-around" method with the problematic "placement" BGL(s), please let us know.
[
END_EDIT]
GaryGB
