We had run into this exact problem. The issue was that there were duplicate network adapters, both had the same IP and mac address but only one had the parent configuration item while other had the configuration item field as blank. The OOTB script was matching both but selecting one without the parent. That's probably the behavior you are seeing as well. The resolution was to delete the duplicate network adapter, the one without the parent CI and let the sync happen again. Also, you have to look directly in the network adapter table "cmdb_ci_network_adapter_list.do", and check for the duplicates.