You are not alone! I am having exactly the same issue. After doing some research it looks like the problem lays in that pulseaudio does not support digital audio passthrough.
I still don-t want to give up because the previous link is a bit old and a fix could have been found. But I am not aware of it yet.
Just to confirm, that our issue is exactly the same. When you test your speakers with the sound prefereneces tool, do you hear the right speaker test coming out of the subwoofer?