Just as another data point, I recently checked in and saw that at the summary, I was in First/O but with a Coach seat assignment. I brought up the change seat option and it showed the First Class cabin but all the seats were taken.
I probably should have called - I wonder if there might've been an available "blocked" seat in Row 1... Anyway, I was running late so I continued the check-in process and it ended up printing a coach boarding pass for that segment with the coach seat assignment shown originally. Looking back at the reservation after the trip, it reverted to Coach/original fare class. Definitely strange.
Aside from a weather cancellation/rebooking, this was the only missed upgrade so far this year so I really can't complain. That being said, I definitely think their upgrade process still has a few IT gremlins lurking about...