It's either a firmware issue or settings. Many apps do not honor TV settings and you need to set the audio in the app.
I've got 65" KS800D that is hooked up to my surround sound receiver via optical. That works fine for my PlayStation 4 which is hooked up in the first hdmi port, and also works fine when I run an audio test through the settings menu on the tv.
However, when i try to watch Netflix or Amazon or any video app through the smart menu, the speakers turn off and nothing will play until I go back to the PlayStation. Any ideas?