Skipping the intro leads to audio desync on Nvidia Shield

I’m really glad the issue got fixed for you. I can report the same thing, haven’t had any issues with the desync since turning Dolby audio processing off.

It seems like maybe your issue could be unrelated. Are you experiencing stutters during playback? Are you trying to play 4K content with seamless branching?
If so, maybe these would be of help to you:

Also, it’s a bit risky, but you could try applying for the Nvidia Shield Hotfix and try that? The risky part is, once you install the Hotfix, you can’t go back, so I would definitely read more about the Hotfix before doing this. You can apply and read more on Nvidia’s official forum here:

https://www.nvidia.com/en-us/geforce/forums/shield-tv/9/522242/shield-experience-upgrade-911-hotfix-image/

Edit: I have also read some posts about Framerate/Resolution match settings being part of the problem potentially, so @Basche you could also try playing with those settings around.