Sometimes shipments are viewable in the Shipments section or when linked from an Invoice but they don't appear in the Network Analysis charts.
This is all about the ship date. If there is no ship date associated with the shipment then it is not included in the Network Analysis charts. This is because all of Network Analysis is filtered by the ship date; by default the last 12 months of ship dates.
The best way to resolve this is to ensure that ship dates are present on the files that are sent to the 7bridges software (invoices or shipment reports).