Called Amex late last night to get an update.

Apparently the rate plan code Amex used had a different value in the hotels system. So to the hotel, I hadn't paid for my room in it's entirety. They didn't know about the AMEX rate so when I (and AMEX) asked them about the difference, they just assumed we were talking about the resort fees which is why they kept saying the additional cost was the resort fees.

Some silver lining: they got the FHR credits applied correctly the first time without needing to argue over it!