Reference number not populating

We seem to be having an issue where on the web version of ShipRush, the reference number (Ebay order number, or Amazon order number) isn't showing up in the "Reference" field like it did on the standalone Shiprush software.

All orders where we've used the web version are not showing any reference number info on our bills from FedEx, for example. All orders where we used the old software still are.

Are we possibly missing a setting somewhere, or is this a possible glitch?

Thanks!