The F4215 Shipment Header is created either from SO Entry, PO Entry or Shipment Creation. The F4217 Shipment Reference is not created by default (as I understand it), I believe it is only manually maintainable via Shipment References program (row exit on Shipment Status Inquiry P4947).
As you believe that these records pre-date your Transport system setup I suggest that you may have some mods. Check the pre-dated records in these files with UTB and hopefully the Program ID field will give you some hint as to where these records are coming from.
Regards,