This is a Hilton glitch. If anyone at the hotel changes the reservation you made in any way, for example a room upgrade, the AMEX bonus does not post.The diamond desk told me that they all are aware of this but can't do anything more than to add the bonus to the account when I call in.
This happens to me so frequently that I just wait till I accumulate 4-5 stays and call the Diamond desk to have the points added to my account. No problem. I don't mind since the usual reason I don't receive the bonus is because I have been upgraded to a suite.