How were you using Dolby Atmos if you haven't configured your Denon to Atmos? In order to enable the Atmos extension of the Dolby True HD codec, you must enable the correct speakers in the setup, otherwise, the "Atmos Soundrack" is simply played as Dolby True HD 5.1 (or 7.1). In other words, the Atmos extension gets folded back into the Dolby True HD 5.1/7.1 stream if the Atmos decoder is not detected/enabled in the receiver.

Sounds like you have a source issue if playing any other content seems to work.