The advanced furnace has audio pops when it is working. Each time the cycle ends, it pops. There's a soft pop and a loud pop. It's very easy to hear if you are wearing headphones and zoomed in near a furnace.

Yes, this happens when the furnace has a big bonus to speed. Unfortunately, this cannot be fixed, since there is no command that would turn off the dependence of sound on speed (or I just could not find this command).
But I will try to reduce this effect in the next update.

If the sound of the furnace is custom, you can probably fade the sound in at the start and out at the end to alleviate some of this.

I'm unconvinced that the speed bonus causes it. As I test, I removed all inputs to the machines. For this specific test, it was with the advanced assembling machine. In other words, only the idle sound is present.

At the end of the idle sound loop, there is a audio pop.