We recently stayed at the JW Marriott in Las Vegas. The attached casino gave us a special rate. As result, we did not get credit for the "stay".
The only reason we accepted the special rate was because last year I called Marriot Rewards and was told that you will not get credit for the "stay" if you book thru a third party ie; Travelocity, Expedia etc. BUT that getting special rate thru attached casino will get you credit for the "stay".
Did you reach out to Marriott to confirm that the rate given to you was the reason the stay/night credit didn't post? Marriott's website does indicate that some corporate rates will not qualify for this.