So, my kubuntu 16.04 (+ Neon LTE repository) has upgraded to new HWE with kernel 4.13 and now both my microphone and headphone inputs are detected only at boot time or when system resumes from suspend.
pavucontrol displays microphone or headphone as plugged in (unplugged) and it won't change as you insert or remove jacks. The only way to change that state is to reboot or suspend/resume. Not sure if someone else has this issue or what issue it is (where am I to report it if it is has to be reported).
hdajacksensetest reports proper information about jacks state.