Clicking sound or short sound cut every few seconds when using Apple TV and dolby atmos receiver?

I have been having similar issues with YouTube and Apple TV. In my case, center channel dropout and other anomalies in 5.1 or better audio. I think I have it fixed now, but time will tell. Here is how:

Start a video within YouTube that has 5.1 or better sound.

Go to the tool bar of the video and at the far right you will see a gear, for settings.

Click it

Now you will see a menu with an option for decoding 5.1 sound. If it is checked, UNCHECK 5.1 sound. You should notice an immediate improvement. I know this seems counterintuitive.

I think the lost sound issue was the result of conflict between Apple TV, my AV receiver, and YouTube app over which is decoding the mix. Once I took YouTube out of that group, my Apple TV 4K (2nd gen) and AV receiver are now interfacing better on multichannel decoding.

You don't provide info about the audio attributes of the content that's working for you and that which is failing. It's not a Dolby Atmos problem because YouTube doesn't stream atmos content (despite some of the uploaded videos that claim to contain Atmos audio).

That said, your receiver is a decade-old design and one of the first that offered Dolby Atmos support with a post-release firmware update, so I would make sure it has Pioneer's recommended firmware from 2014 and temper my expectations about how well it will work with modern Atmos content via the ATV4K (which decodes atmos streams and sends the uncompressed multichannel audio with Dolby MAT to your receiver).

Does your ATV4K automatically report Dolby Atmos support in the Video and Audio Settings when connected to the Pioneer? Anyway, here's Apple's support article about getting things setup: Set up Dolby Atmos or surround sound on Apple TV with a sound bar or AV receiver - Apple Support.

Thanks for reaching out SwisSebastien,

It sounds like you're having some trouble with viewing YouTube content on your Apple TV, but not Apple TV+ content. We can help.

You've done a great job of isolating the issue so far, and it looks like you may need to contact YouTube for help if the issue seems to only occur with their content. You can check out this link to Change the quality of your video.

Hope that helps.

Take care.