I had the issue of alsa starting with volumes muted on my normal box, running alsamixer showed all channels set to mute. The issue on my box was a stale /etc/asound.state file in my backup. I don't know if it got corrupted or it was from another machine, but removing it and starting fresh fixed it.
I have not tried to find why my laptop starts with certain channels muted, but this at least helped on my desktop.