Robin is correct it looks to be potentially a VLC Libraries issue.
Although I would think Robin might need to take another look into this, as I suspect there maybe an issue with the latest VLC Library installer.
What you have is scenery from Lawrie Roache's, South Pacific FlightSim Scenery
from August 2012 4X his collection of sceneries such as Martins Bay-4X.zip file from the initial pics shown, these are of Martins Bay Lodge Airfield NZMJ and the second posting lot of pics shown are from the Mercer-4X.zip file for Mercer Airfield NZME
At the time when the scenery was created the VLC Library Installer was version 1.2 from May 2012
I downloaded at the time as VLClibrariesInstall1_2.zip
Then in December 2012 VLC Library installer was released to version 1.3
I downloaded at the time as VLClibrariesInstall1_3.zip
It would appear that the Missing Building objects are found in the VLC Library installer versions 1.2 and 1.3
Subsequent VLC Library installer iterations released in 2014 with a Dual FSX and Prepar3D as version 1.4
I downloaded as VLClibrariesDual1_4.zip and later another version 1.41 was released in July 2016 that I downloaded as VLClibrariesMultiInstall_1_41.zip
Although when downloaded from Vector Land Class Libraries
it shows as the current version 1.4 when you download and Unzip you will find just the installer VLClibrariesInstall.exe when Run as adminstrator the Installer Setup wizard is for Vector Land Class Libraries 1.46
As I have both previously installed Lawrie Roache's Martins Bay-4X and Mercer-4X sometime ago I thought I had better check my own setup and found that after, I had updated to the latest VLC Libraries done way back in late 2016 using the file VLClibrariesMultiInstall_1_41.zip
I found that I was getting the same results with missing buildings, fences, vegetation etc, from where they should be in the example pics.
I have run the VLClibrariesuninst.exe and removed, uninstalled the VLC Library and since I have a backup copy of the the older Library VLClibrariesInstall1_3.zip have re-installed and checked again.
Bingo I now have the missing buildings showing up.
It's a bit of mystery so wondering if Robin could perhaps shed some light or check back with the different VLC Libarary installer iterations as Timmo's website for the VLC Libraries 1.4 says that all libraries are backwards compatible with previous versions (V1.0, V1.1, V1.2, 1.3).
Robin might want to do some checking of his own, if he has the older VLC Library installer versions 1.2 and 1.3
I also checked the documentation Read Me.txt and Mercer-4X INSTALL.doc and ensured that I had moved the BGL file named “AFX_NZME_ALT.bgl” into the FSX/Scenery/World/Scenery
Not sure if anyone else has come across VLC Library issues like this with older FSX scenery, seems like it might be getting a little outdated now that Vector Land Class has gone freeware with not much support these days with the advent of newer modern x64 bit Flight Sims.