When watching content in Hulu, Netflix, HBO Go, etc. that is encoded with stereo audio, I want the PS4 to output stereo (2.0 channel) audio through HDMI. It doesn't seem to matter whether I select PCM, DTS, or DD, it always outputs 6 channels with 4 channels of silence. The problem is that for a video with only 2 channels of audio, the other channels are mute. This makes it impossible to use my receiver's Pro Logic II feature to up mix and use all my speakers.
This sounds like a firmware bug to me, try contacting Sony about the issue and have them fix it the proper way.
In the meantime the PS4 does support external USB sound cards. The cheapest stereo sound cards usually only have analog and only passable audio quality, but I've found they're pretty handy for locating sound issues.
I haven't personally tried this on my PS4, but a quick Google search suggests pretty much any generic USB sound card should work. http://www.reddit.com/r/PS4/comments/1rfa7r/list_of_working_ps4_headsets/
It could also be part of this bug, but I don't have the hardware to test for myself: http://www.ign.com/wikis/playstation-4/PS4_Audio_Problems