The layout netlist shows only numbers for the nets, no names at all. This might be related to your missing ports. Calibre LVS usually looks for text objects in the layout database to use for net names and ports. Can you check to see if your drawn layout has text for those names you wanted? The text in the layout database will need to be on the same layer/texttype expected by the rule file used for connectivity extraction phase of LVS. Any statement in the rule file containing the word "TEXT" might provide clues to the desired layers to use.