I had a similar thing happen to me on a GRU-MIA-BOS itinerary last summer. The SWU for the GRU-MIA portion cleared a month in advance, and I was waitlisted for the MIA-BOS segment. Upon equipment swap from an International-configured 757 to a 24-seat domestic First-configured 757, the SWU for the domestic cleared about three hours before departure, but when it did, it listed as "Complimentary" rather than "Systemwide Upgrade."
All's well that ends well, but the concern is if, on the airport upgrade list, the SWU request isn't carrying over, and it's waitlisting at the airport as a Complimentary upgrade, therefore putting someone lower on the list than they would otherwise be with the SWU request properly put in place. Not sure if that's what happened, or if the agent clearing the upgrades at the airport just opened R space and cleared the list in order.