First, I have had trouble getting a last minute reservation in SF, too, especially if one of the big conventions is in the city. I believe the poster.
Second, I had a very similar situation with a Hilton family hotel. Their system had been down throughout the day. I called the hotel directly and they told me to keep trying online. Eventually I got a reservation with a confirmation email. When I got to the hotel desk clerk gave me a similar story that they were not going to honor the reservation. I called the 800 number, they reached out to the hotel manager and I immediately posted on TA. Ultimately they found me a room at the hotel, did wind up walking others that night, apologized and gave me a buck load of points.
TA works well for situations like yours. Post there and the hotel and the chain will get in touch with you fast.