In Ubuntu 16.04 sound menu, choosing "Analog Output" option don't allow to select 2.0 output for stereo speakers, only 4.0, 5.1 or 7.1. There is also a new "Headphones" option in the sound menu for the same sound card. This didn't happen in Ubuntu 14.04.
UPDATE: Still not fixed but there is a workaround: https://superuser.com/questions/1117482/pulseaudio-controls-wrong-volume-bar-xonar-dsx
Just run these commands in a terminal:
$ sudo mv /usr/share/pulseaudio/alsa-mixer/paths/analog-output-headphones.conf /usr/share/pulseaudio/alsa-mixer/paths/analog-output-headphones.conf.backup
$ sudo touch /usr/share/pulseaudio/alsa-mixer/paths/analog-output-headphones.conf