I am far far from being a vLSO expert (I don't mess with it much. The AI LSO's it uses have it in for me, I swear. Very often
), but is it possible your sceneries are not someplace vLSO "looks" for them? I know FSX lets you put sceneries almost anywhere, but does vLSO only look in specific places, maybe? Most people put their additional scenery into the Add-On Scenery folder in the main FSX folder. Could it be, perhaps, that vLSO looks there for it, only?
I don't know where you installed your sceneries, or the IFOLS Trailer add-on (if you use it). Maybe, also, the priority needs to be higher or lower? Maybe you don't have high enough (or low) in the Scenery.cfg. Again, I am guessing here. I don't have the faintest idea if these guesses have any validity at all.
I hope Paddles will weigh in on this. I am just throwing WAGs out there.
Pat☺