Trainz/Transparent Windows using Blender< Trainz
Scenery objects treat transparency differently to rolling stock. Only other scenery objects can be seen through transparent scenery objects.
For Blender settings see Torsten's comments in this thread in the Trainz forum labeled "Transparent and semi- transparent meshes with Blender 2.65":
Creating a transparent file in GIMP then painting it with opacity of around 30% seems to work.