Okay, to start off, in some cases, Geforce Experience isn't actually started up and shadowplay is just running on its own. I'd suggest making sure Geforce Experience is fully updated (not your drivers) and running, from then we can start with trial & error.
1. Simple update and restart, it could fix a lot of things, also making sure your default audio is set to your headphones, Geforce Experience automatically chooses the default audio.
2. (disable mic settings) Press your hotkey to open your in-game overlay, and disable your mic on the bottom right.
3. There's a chance in your settings ( the gear at the bottom right in the in-game overlay) that your system's audio tracks are separated and not a single track, if it's the opposite, then simply click separated and restart your computer.
4. Go to your sound settings, make sure everything is set to default, if all else fails, try using a different audio device. right click the volume button, open sound settings, scroll down to Advanced sound options and config your PC from there, remember to restart PC.