I do have same problem with my Apple TV 4K and Yamaha RX-A3040, apparently the comments above are not really valid and pointing towards issue with receiver, and there have been number of posts and issues reported on different forums with the same issue, and specific bug report for Apple has been created, as there are some missing flags in the Atmos stream sent to receiver from ATV. This needs to be fixed by Apple, however so far nothing has been done which is very disappointing and frustrating.
Below is the copy of the bug report from another forum, with specifics - additionally I will clarify that TV OS version below is the older one as I have the newest and the issue is still there.
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Non-compliant Atmos stream / lack of channel status information
According to Yamaha, PCM/Atmos streams are apparently non-compliant due to the source device (Apply TV) not transmitting channel status information. This is causing total signal failures on multiple devices (known to occur on Yamaha, Pioneer, and Onkyo amplifiers, have replicated on Yamaha RX-V2077 / RX-A1040 / RX-A2040 / RX-A3040). Replication details are below:
Summary:
Atmos streams sent from Netflix by the Apple TV 4K to the Yamaha RX-VX077 / RX-AX040 series of amplifiers fail to be recognised or decoded. When Atmos is set to "on" within the Apple TV settings and an Atmos media source is selected for playback (e.g. Lost in Space on Netflix), the amplifier fails to recognise the signal as a valid Atmos stream. The amplifier is Atmos certified and files and disc-based media played from other devices (e.g. WD-TV via SMB, Blu-ray discs with native content) are successfully recognised and decoded as an Atmos track by the amplifier.
Turning Atmos compatibility off within the Apple TV settings re-enables audio but is only recognised as a PCM track with no Atmos compatibility.
Steps to Reproduce:
Enable Atmos compatibility within the Apple TV 4K settings. Play an Atmos-enabled media source and output the audio to the Yamaha amplifier.
Expected Results:
The resulting audio track should be recognised as an Atmos track by the amplifier and decoded with positional metadata.
Actual Results:
The amplifier fails to recognise the soundtrack and outputs no audio.
Version/Build:
Apple TV 4K (tvOS 12.0.1). Amplifier firmware release 1.98.
Configuration:
See above.