I have no idea why no-one has suggested this, Iain. Download the SceneryConfig Editor and run it: it will fix your problem.

 

https://dl.dropbox.c...aller-1.1.0.exe

This helped my problem and helped fix alot of duplicate sceneries that were causing me problems with scenery not showing up and certain airports lagging. thank you for this piece of advice.

i know this topic is old but i'm having the same issue too and delete all the FileList.dat files in
C:\ProgramData\Microsoft\FSX\SceneryIndexes\ does not help..

 

it all started after i installed the modifications from this video ..

 

 

also i have installed GSX