Interesting... This stay is listed on my account under HHonors Hotel Activity. There are no points attached to it but when I open it up there is nothing marked next to "Preferred Partner" where it would normally say "HH". It also says quite clearly "Discount Stay: No".
It's the only stay in there that doesn't have HH marked next to Preferred Partner, so that has to be the problem. I notice that I even got points for some of my reward stays so find it very hard to believe that I should get nothing back for a $3,000 bill.