I have this issue since I started using my SPDIF audio output. Every time an audio sample is started or stopped, i hear a loud pop. Even with repeated system notifications: "POP sound POP".
The same thing, on analog output, happens only at boot time (I suspect when the audio chip is initialized).
I don't hear any pop noise when I have a constant stream of sound. When playing a sound, it's a bit delayed and I miss the first fractions of second of it.
Could it be that the system is turning on and off the audio device every time a sound is played? Maybe some energy management routine that shuts off the device?
If so, is there a way to prevent this?