Changing the opacity of an pipeline filter/source whose representation is set to "3D Glyphs" to a value less than 1.0 results in incorrect rendering. For example, consider this screen shot:

NB: The ExtractSurface1 filter in both cases shows the actual faces of the box. In the top view, the spheres are rendered by Box1 using the glyph mapper. In the bottom view, the spheres are rendered by Glyph1 with its representation set to Surface. The opacity is set to 0.7 for both Box1 and Glyph1.