I'm having the same problem. Any joy? As far as I can tell, it's happening when the audio interface "wakes us" and "goes to sleep" (power-saving mode). It's so frustrating! Does anyone know how to turn OFF the power-saving mode of the audio interface.
I have tested with multiple external speakers plugged into the headphone jack, and they ALL have the same sound.
To be clear, though, this is not a sound file being played. This is a "popping" sound that resembled the noise you might hear when plugging in a sterio or headphones to a live source. I'm fairly certain it's a result of a current being sent to the speaker as the audio sub-system powers up and then powers down about 10 seconds after the computer plays a sound.
The first "pop" is a half-second before the computer plays a sound, and the second "pop" is about 10 seconds after no other sounds have been played.
Mac Mini, Mid-2011, 2.5 GHz Intel Core i5.