FHR benefits missing on Equinox Hotel stay, charged for late checkout

Booked the Equinox Hotel for my birthday through Amex concierge since it’s part of Fine Hotels & Resorts. The agent listed all the usual perks, including 4pm checkout. But on checkout day, the hotel called saying housekeeping found my stuff still there and that I’d be charged for late checkout. Turns out they had my booking listed as Expedia and no FHR benefits applied. Filed a claim, but has anyone else had this happen where the benefits just didn’t attach?