I had the same problem. The navigation sound work but with delay, i press bottom and the sound play 2 seconds later. The video screen saver is not heard. The volume control although it changes it stays at zero. But the sound in the games is good.
I have tried all the options of "Audio Card" "Audio Device", but the only one I hear something is heard with a lot of lag.
This happened to me after I had updated the Emulation Station. Before updating it worked fine.