I am having the same issue. I have called Apple tech support and was told to reset the ATV 4. This did resolve my issue but only for a few days and now the audio output is incorrect again. My Onkyo receiver will detect a stereo 2 ch signal and automatically switch to stereo mode, or back to Dolby Digital when watching a movie. After a couple of days of using the ATV4 my receiver only says multi-channel. Again, I reset my ATV4 and the problem is resolved with sound outputting the way it should but only a for a day or two.
My receiver is an Onkyo TX-NR616, with the latest firmware upgrade (thought maybe it was my receiver). If I plug in my ATV 3, I have no audio problems and everything plays the way it should. Movies and music sound like crap because the receiver is not able to output correctly with mixed channel output coming from ATV4.
Really disappointed that Apple could not get this right as it worked perfectly on ATV3. I don't want to keep factory resetting the unit every few days to get the auto sound output working correctly.
Also, to the users who have forced the setting to Dolby Surround in the ATV menu, you are not getting true Dolby Digital sound, this just tricks your receiver to show Dolby Digital but not all channels output correctly as another user has stated.