I had the same issue (or similar issue, at least) with audio. I can tell you what worked for me, but results may vary.
What I did was lower all the graphics settings. Even though I was running it fine before at around 60fps, the sound was crappy in the ways you described. My first guess was that because I was using the adaptive resolution option, that might have some impact on the game's ability to render sound(???). I lowered all the settings, and even lowered the resolution to 1600 by 900, and that seemed to work for me. I guess somehow the SFX are tied in some way to graphics. I have no clue how or why, but it worked for me. Let me know if it's the same for you. The game looks crappier but at least it runs well and I can actually hear what's going on.