Special Nets (typically power nets) and Signal Nets (also referred to as regular nets) are different object types in the Encounter database. So in the streamOut mapping file you'll specify them separately although you can map them to the same GDS layer number and datatype:
layerName NET gdsNum dataType # This is for signal nets
layerName SNET gdsNum dataType # This for special nets
If the mapping files are correct and you have the layers displayed properly in Virtuoso, I'm not sure why you would not see them. I suggest opening a Service Request to get help with debugging this further.