I have a rather complex setup here, so while I'm usually pretty good at finding these problems, I don't have a clue where to start. There are a lot of places here (not all relevant to this site) that could cause the problem. Hopefully someone here has an idea.
I have a computer set up to operate in my car, as a replacement for the stock electronics in the dash. It runs a modified version of Debian Testing, connected to a Diamond XS71U USB sound "card", from which a Toslink cable runs to a fiber-to-RCA adapter, connected to an amplifier. (The Toslink cable eliminated a particularly annoying ground loop problem.)
The sound system clearly works, because some things sound perfect. However, when I play any MP3 file or about 50% of the M4A files I have, there is a constant popping through the speakers, very regular in time, about two pops per second. The pops vary in amplitude, both randomly AND with the loudness of the music, but are very loud.
The sound files are being played via mplayer through straight ALSA (no PulseAudio), with the sound running through the softvol plugin to allow volume control on the digital audio.
