I have managed to make the problem disappear. And reappear.

On a fresh reboot, if I go to menu->System->Preferences->Sound, set one
of the "Sound Playback" drop boxes to be the ALSA digital output, and
hit the "test" button, the sine wave is usually (if not always)
distorted. If I run alsamixer in a terminal while a distorted sound is
playing and mute and then unmute the digital output, the distortion
disappears. In general, I can make the described distortion disappear
using this method. For example when I run gnome-listen and the loud
parts in the music are incorrectly distorting, muting/unmuting the
digital output fixes it.

As long as the sound remains continuous, the distortion stays away.
However, if I stop sound playback, and start it up later, the distortion
sometimes reappears. In the sound preferences panel, this happens after
an indeterminate number of hitting "test" followed by "okay". Distortion
also reappears if I "fix" the disortion issue while playing test sounds
in the sound settings dialog, then close that dialog and start something
playing using gnome-listen, it is always distorted.

Also, once I use the sound prefs dialog or listen to "make" my sound
distorted, sound playback through "aplay" is also distorted. If I then
mute/unmute the digital output, "aplay" will then play undistorted
sound. Seems like this proves that this is an ALSA problem, no?

So as of right now, loud passages of sound audibly distort, and the only
way to "fix" it is to mute/unmute the digital output. Help?

-- 
ALSA SPDIF Digital ourput clipping / crackling during playback
https://bugs.launchpad.net/bugs/359361
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