I had the same problem today. I was trying to put vlc playing in 5.1, and the 
same thing happened. Now I only have sound from the analogue output 
(headphones) or when I play anything with AC3 sound with totem. Everything was 
working perfectly before that. I've tried to put vlc with the original 
configuration, reconfiguring alsa, fiddle with the mixer settings, etc, but 
nothing worked... I will try to reinstall alsa.
My specs are similar 
ASUS P4P800-E, SB Live with SPDIF to amplifier, Ubuntu Feisty with latest kernel

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