Modifying layer transparency for extruded features in ArcScene through Layer Properties and the Layer Transparency tool result in improper handling of layer transparency.
To have the transparency perform correctly, set the transparency to 0% and remove the extrusion, then re-apply the extrusion and define the transparency as desired. Use the same method for changing the transparency value (e.g. if it was modified via Layer Tranparency tool, then keep using the tool).