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The transparency property of a layer is lost when exported via a scene to VRML if it is symbolized with any picture fill symbols.
There is a limitation in the way VRML handles transparency: the transparency of the material (the percentage of transparency of the layer) cannot be combined with the transparency of the texture (picture fill symbol or raster). The texture transparency is used when it comes from a picture fill symbol (so objects like trees have the correct transparency). The layer's transparency percentage will have no effect in this case.
Use the symbol's transparency property rather than the layers' when exporting to VRML.