Just want to chime in with my experience.
Before my two ATV4's I had an ATV3 and an ATV2 both set to Dolby Surround in settings with optical out for audio and HDMI for the video from the ATV to their respective receivers. I got proper 5.1.
When I got my ATV4's I was initially upset that the optical out was removed, for no perceivable reason, I might add, so now am doing HDMI for both audio and video...
Anyway, I have found that I was only getting a stereo signal even though I had set the audio to Dolby Surround. My receivers were also not reporting PCM stereo either. Both would simply display Decoder Off.
My solution was simple though, I changed the audio setting to Auto, and then played up a film. The receiver came to life and switched to PCM. I then went back into setting and changed the audio back to Dolby Surround. Went and played the same film, and boom - full glorious 5.1 Dolby Digital Surround, receiver reporting properly DDII Movie decode as I had it set.
It seems like it was just stuck somehow. I tried the same on the other one and got the same result. I actually had to play media with the Auto setting on first and then go back and change to Dolby Surround again in order for it to "awaken."
Hope this helps people out there pulling their hair out!
- Edit!
Have realised that it appears this is a recurring issue - I had to repeat these steps again today to get surround sound working...it is extremely irritating!!!