When creating a multi-package shipment in UPS Shipping Manager from an invoice, the first package has a reference number associated with it, but additional packages do not.
This is as designed for ALL multiparcel shipments: The first tracking no, which is the "master" tracking number is saved. IOW, the #1 track is sufficient for any tracking or claim needs.
This is a display issue only. When you print your shipping labels, the reference number will appear on all labels for all packages in the multi-package shipment.