The root problem: for some reason, on boot, Ubuntu 14.04 disables (mutes) the S/PDIF output on my sound card.
This question and its answers indicate that
sudo alsactl store will store the alsamixer settings once I've unmuted the S/PDIF output, but on boot, the S/PDIF output is muted again.
/var/lib/alsa/asound.state (pastebin) there is one PDIF entry, which I've set to "true" and saved; this has resulted in solving auto-mute for my "Phantom Jack" but there's no other entry for the "true" S/PDIF in asound.state that I can manually adjust.
There's also an empty
/var/lib/alsa/asound.state.lock file (11 bytes, blank in gedit) in the
/alsa/ directory. Is this something I should be dealing with?