I had the same thing happen to me a few days ago. I was within the silver upgrade window, got an email saying that no first class seats were available, but then I checked the seat map through the booking portal and it showed 4 empty first class seats. Since it was ~40 hours prior to departure and check-in was not available yet, I just called US reservations, and the ticket agent looked up my ticket and put me in first class.
Edit: I posted this on another thread and got a few replies saying that US hold first seats for revenue prior to flights even within preferred upgrade windows, so once those seats are taken away from revenue they are given as upgrades based on the priority list. They certainly know better than me.