Yep, I did make those copies in to the Malta folders. Here is my scenery cfg:
[Area.011]
Title=FS2000_props
Local=Scenedb\fs2kprop
Active=TRUE
Layer=11
Required=TRUE
Remote=
[Area.012]
Title=DEM8
Local=SCENEDB\DEM8
Remote=
Active=TRUE
Required=FALSE
Layer=13
[Area.013]
Title=DEM mesh
Local=SCENEDB\DEM mesh
Remote=
Active=TRUE
Required=FALSE
Layer=12
[Area.014]
Title=Global_Exclude
Local=SCENEDB\Global_Exclude
Remote=
Active=TRUE
Required=FALSE
Layer=14
[Area.015]
Title=cfs2_eurw_LC_su_BETA4
Local=SCENEDB\cfs2_eurw_LC_su_BETA4
Remote=
Active=TRUE
Required=FALSE
Layer=15
[Area.016]
Title=Eurw
Local=SCENEDB\Eurw
Remote=
Active=TRUE
Required=FALSE
Layer=16
[Area.017]
Title=Afnor_Scen
Local=SCENEDB\Afnor_Scen
Remote=
Active=TRUE
Required=FALSE
Layer=18
[Area.018]
Title=Afnor_Bases
Local=SCENEDB\Afnor_Bases
Remote=
Active=TRUE
Required=FALSE
Layer=17
[Area.019]
Title=Gibraltar43
Local=SCENEDB\Gibraltar43
Remote=
Active=TRUE
Required=FALSE
Layer=19
[Area.020]
Title=Casbah_cities
Local=SCENEDB\Casbah_cities
Remote=
Active=TRUE
Required=FALSE
Layer=22
[Area.021]
Title=Fringing&Cay Reef
Local=SCENEDB\Fringing&Cay Reef
Remote=
Active=TRUE
Required=FALSE
Layer=20
[Area.022]
Title=Stream_Lake
Local=SCENEDB\Stream_Lake
Remote=
Active=TRUE
Required=FALSE
Layer=21
[Area.023]
Title=LandClassMalta
Local=SCENEDB\LandClassMalta
Remote=
Active=TRUE
Required=FALSE
Layer=23
[Area.024]
Title=Malta2
Local=SCENEDB\Malta2
Remote=
Active=TRUE
Required=FALSE
Layer=24
Flatten.0=0,N35 50,E14 32,N35 49,E14 34,N35 48,E14 34,N35 49,E14 32
[Area.025]
Title=Malta_BSK_V2
Local=SCENEDB\Malta_BSK_V2
Remote=
Active=TRUE
Required=FALSE
Layer=25
[Area.026]
Title=Desert_scen
Local=SCENEDB\Desert_scen
Remote=
Active=TRUE