Hi, been pulling my hair out over this,
My system is GTX 750 Ti SC plumbed into a MSI Z170i mobo with an i5 6600k cpu running Win10.
Connected via HDMI to an Onkyo receiver.
 
My issue is that audio seems fine in windows but when I load a game the audio is not there. I can get it back by switching to windows and by changing the sample rate within playback devices, applying it and the audio comes back on in game. Occasionally the audio is there in game to start with but then vanishes at a load screen or cut scene.
It's happening on a fresh install, I've reinstalled fully trying to solve this. I've tried fully removing drivers with DDcleaner and numerous other delete/re installations of drivers without any luck.
I've also tried disabling onboard audio, and even did the reinstall last time with it disabled.
 
I had the gtx running on another mobo without this issue so is it a driver conflict? Can't find anything online that's helped. 
 
Installed on a SSD, can an issue survive a quick format on an ssd?
 
Appreciate any advice given.  
 

Zuhl3156
I would try a different audio input to your receiver. My Sony Home Theater system doesn't have an HDMI input but I have no problems getting audio through a fiber-optic or RCA input. Just my thoughts on the matter as I am no expert on the subject by any means.

 
Thanks Zuhl3156 I'm pretty sure the amp and hdmi cable are ok, used the same ones on an earlier build with same GPU for months without issue. I have changed the hdmi cable along the way to test as have heard they can cause issues but that didn't help.
I've got a S/PDIF coming, hopefully the onboard audio is more reliable.