Update: i may have found workaround, see at the end.
I have confirmed this behavior with Ubuntu Gnome 16.04 and Ubuntu 17.10 on my machine. My soundcard and pulseaudio work fine, but the only way to choose proper sound output (e.g. headphones) is to use pavucontrol, gnome's sound applet shows only one output - digital S/PDIF.
I was previously using Ubuntu MATE 16.04 and it had no such problem. However, it is present with Ubuntu MATE 17.10.
Edit: After some research i have found some interesting suggestion. Particularly this question Headphone jack not working? has an answer that leads to these instructions: https://pricklytech.wordpress.com/2012/08/27/ubuntu-12-04-dell-vostro-3750-no-sound-when-headphones-are-plugged-in-fixed/
Following them i edited file /usr/share/pulseaudio/alsa-mixer/paths/analog-output-headphones.conf, simply commented out every line that started with "required-any". So, find and replace in text editor "required-any" to "#required-any". After that i restarted pulseaudio, using command "pulseaudio -k".
Now headphones show in gnome's sound settings, and i can choose it and it works!
Now i really need help. Unfortunately, I'm out of my depth here, I don't know what these files at /usr/share/pulseaudio/alsa-mixer/paths/ are and what should be proper solution, but it is clear they should be involved somehow.