Amazon replied to me and said the following:
"Please note that this shipment is created via Send to Amazon (Seller Central UI), and so the API updateShipmentTrackingDetails cannot be used to provide tracking details.

Please use Seller Central to update tracking details for this shipment, and use the updateShipmentTrackingDetails API only for API created shipments."

This explains why it doesn't work for all my shipments, but makes it even more confusing as to why they did work since all of our shipments are made in seller central UI.