Yes, check the receiver settings. My problem was I had the speakers configured as 5.1 (which i thought was a valid ATMOS config). Changing it to 7.1 made atmos start working.
No steaming services offer Dolby Atmos in lossless form which would be in the format of Dolby True HD, Netlfix, Apple TV, Prime & Disney Plus stream Atmos in Dolby Digital Plus which is lossy. you can only get lossless via Bluray
There has to be a 3rd number in your speaker config, i.e. 5.1.4 and not just 5.1, or it's not Atmos. The 3rd number is height channels, which Atmos REQUIRES to work.
Also the only Yamahas that can apply DSP effects to Atmos are the super high end pre-pros (CX-A5100 / 5200). I'm not sure what the behavior is if you try to use Atmos with a DSP mode selected on lower models, but this might be why your Yamahas aren't playing Atmos sometimes and are other times. Try setting the DSP to "straight".