I suffer the EXACT same problem as the OP suffers from, I also have the same motherboard, the z170 pro gaming, it doesnt always make that sound i.e when playing music it seems ok but anything related to windows sounds like ding, or even testing by using the windows sound icon next to your clock, select sound devices and then select speakers and then double click on it and select the advanced tab and then push test, you will hear sound in your left ear and then right, it crackles just as the sound begins and ends in each ear.
I have even noticed interference when moving my mouse, very rarely though, its just the crackling thats getting to me.
I also cant believe that this board has had 10 bios updates in the space of a few months, which tells me it was rushed out the door to meet the release of skylake cpus,no wonder they were giving away a pair of cerebus headsets with them, oh the irony, give us free headsets to make up for the dodgy built in sound.
Crackling on my board happens from the rear line out which is connected to my soundbar and the front panel header is connected with the HD Audio connector instead of the ac97 one and the crackling happens on both.
Have formatted/reinstalled windows 7 twice, just the bare minimum, chipset,vga and audio then lan, also installed win 10 three times since it only takes 15-20 minutes tops and still the same problem. Funny thing is the crackling isnt there with the generic MSdrivers, my mobo is one month old and I have a soundcard arriving today so hopefully that cures the problem if not then I will be returning the board to where I bought it from.
TBH i had a funny feeling I would have problems as soon as I ordered another asus board, because going back to the amd 939 days, I had 2 faulty a8n deluxes and out of two a8n32 deluxe mobos only one worked properly, I was sworn off everything asus except for their soundcards and have been a gigabyte mobo fan since then til me getting yet another problematic asus mobo
All my gigabyte boards after socket 939 worked perfect from the get go, even the onboard realtek audio worked perfect, I really regret purchasing another asus mobo as their rma process is a nightmare hence why I am rmaing it via my etailer who are excellent and will test and replace within 7 days, instead of the weeks and weeks that you have to wait for an asus rma.
Either asus or realtek should let us know whats going on as the alc1150 chip isnt exactly new, its a few years old even though asus do call it supremefx 2015.
Its very annoying to have to rma a mobo just because of a dodgy onboard chip And buy a soundcard that is over 100 quid when Ishouldnt have to and its going to severly get in the way of my other addin cards.
whether its as explained by the OP, a power saving feature or a driver problem, something needs done about it ASAP.
EDIT,
Thats bios number 11 just hit the net, damn asus knows this board has MAJOR issues.