I thought I'd already posted the fix here, but I guess not. Luckily, I did write it down in my notes for fixing post-16.04 Ubuntu:
pulseaudio (sigh) powers down the sound card after literally just a few seconds of idle. which makes it "pop" every time it powers back ON, and gtk3's garbage code tries to use the alert sound for absolutely every bloody thing: which triggers ANOTHER pulseaudio bug, where even though the alert is muted PA powers up the sound card to NOT play it...
/etc/pulse/default.pa and comment out this:
### Automatically suspend sinks/sources that become idle for too long
I needed that for a different reason to you, but my guess is it'll solve your problem too.