I, too, have this problem, and after much mucking about, I've discovered that it *is* Flash that's causing the problem. I just don't know how to fix it.
Yesterday (in Karmic) I updated Flash in order to watch videos on Hulu. I lost my sound. I decided it was a good time to upgrade to Lucid, so I did so. Still no sound (and Songbird died).
Nothing is muted in Alsamixer.
I could go into System Settings and play test sounds on the analog outputs (I have no digital sound devices), but YouTube wouldn't play sounds.
Reboot, and sound comes back for a while. I watched a couple vids in MPlayer, and the sound worked fine. Went to sleep, got up... no sound again--the very last thing I was doing last night was watching a video (MPlayer), sound just stopped on it's own.
Today... I muck about with settings some more, try to test sound, and get it to come back in the System Settings test mode. Play a video in MPlayer; it has sound. Try to play Songbird; no sound. Try a video again; it has sound. Try YouTube; no sound. Go back to the same MPlayer video (20 seconds later)... And the sound is dead. Wait a couple minutes (to write this far), test in System Settings and I have sound. Test the MPlayer, I have sound. Play Songbird; no sound. Try the MPlayer again, no sound.
And... to wrap it up, I just tried to test in System Settings, and I get "device does not work" on both of the analog options.
This is *very* frustrating.
I've dug through the forums here and done my best with websearches. This is the only place I've seen this listed. Any help or pointers would be greatly appreciated.