Something similar happened to me last week at JFK. After standing in line and going over the 45 min rule, agent told me I'd have to fly out the following morning.
Then, he apparently changed his mind and sent my luggage thru (which arrived, with me, at SFO).
I wasn't aware of the 45 min rule -- though I sure am now -- and I may have overlooked/over-read it in the past.