Did you try using ALSA Mixer? That touches the audio drivers, and will show all the channels. So it helps when you're checking that the hardware is working.

Most Linuxes use PulseAudio, which, sometimes, is a layer on top of ALSA. Sometimes, it's alongside. Sometimes, the PA software changes a bit, and it'll do things like change the mode in which the device operates.

My setup started out picking digital io from the on-board sound chip. Then, after an update, it started to favor analog full duplex. Then it started to favor analog out and digital in. I had to change it manually.

You can use PulseAudio Volume Control ("pav") to get more control over the audio and change more of the underlying settings.