this is happened to me twice in recent months. Once on JFK-SEA the DL upgrade cleared about 12 midnight the night before 11am flight.
And just last week I was on 9PM JFK-SFO and the UG cleared about 1PM day of departure. JFK-SFO was so strange. I can't believe they held 16 seats until 8 hours before departure. Ludicrous! There was 16 D1 seats available with about 21 on the UG list. They cleared 11 seats early and then cleared 5 more at the gate. in both cases i was well "in the money" on the UG, so the UG processed as expected.
Something else was definitely going in with your reservation. Did you wait list a RUC and then remove that at some point?