An additional note on this. Roughly the same thing happens to mplayer2 (using libav instead of the ffmpeg) but less frequently. A difference is that the cycle of the "stutter" is longer, but the effect of slowing the "heartbeat" LED and the doubling of the players' CPU usage are the same. So I've got similar (mis)behavior with both pianobar/ffmpeg and mplayer2/libav. But I don't at this point know how to go about getting a better diagnosis. No biggie; maybe it will tie into something else.
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