I had the same problem (on a Fedora 6 system), for me upgrading the alsa
drivers and tools to 1.0.14 fixed it. According to
http://alsa.opensrc.org/index.php/Hda older versions may have known
mixer-related problems.

I still need to reload the modules sometimes after playing passthrough
digital audio (especially if the app doesn't quit cleanly), but now get
the sound back properly after that.

-- 
Alsa loses AC'97 SPDIF output in Feisty
https://bugs.launchpad.net/bugs/118861
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