I was having a similar issue of getting stereo over HDMI even on the last of us the only option was 2.0. Rebooted ps4 and then got pcm on my display and the options back in the last of us.
Turned on ps4 later and back to stereo. Here is my theory though. Because I turned on the ps4 and then the receiver and switched over to the right input (defaults to chrome cast for the wife once the receiver is turned off) it only sea aircraft that would accept stereo. But when I rebooted the ps4 again, the receiver was seen as an available 7.1 option and there for gave me all channels.
So try turning on the ps4 as the last thing. Also check your settings both under menu and under settings when you have a bluray playing.
Hope that helps