It's already been placed through Instat Scenery 3. Not working as you can see from the pictures...I had had the same problem when I exported my taxi/runway lights group within MCX as scenery bgl with coordinates. As a solution what worked form me was putting them inside a library and placing them inside the sim with Instant Scenery. I am not sure what changed but that worked for me. Maybe some slight difference effects the drawing order.
I don't think that it has nothing to do with rwy elevation. I have the same problem and with Apron lights as you can see from the photo. The clouds cover the alpha channel of the lights...OK ---1. What is the elevation of your runway custom poly? is it the same as the altitude of the airport? 2. The light model placed on the default scenery has a base to it from the best view I can get yet the one you place on the custom poly is slightly sunk in meaning that the custom poly is slightly higher (as it should ) have you lifted the altitude of the edge light so its sitting ON the customer poly or have you allowed it to sit on the default runway altitude
Thanks,Try downloading Marks Airport Essentials from SOARFLY - That way you'll havce some different ones to test I use them on occasion.
Here is the model in blender. You will see also and the material settings.How did you make your edgelight? Is it really a texture sheet? And what are your material settings for it? Is the runway a custom groundpoly of which the layer is set at a Z-bias of 8?