The point of this blog was to share solutions to obscure problems on the internet in case it happens to help someone experiencing the same thing. So after a 5 year hiatus, here's a short one
Make sure the Speakers playback device for your Blue Yeti is disabled. This is the playback option for playing through a device you plug into the mic's 3.5mm jack. In my use case, I have the HyperX Cloud Alpha headphones and don't require this jack. I had recently enabled the device which looks like it was resetting my mic volume to 50%...no idea why this fixed it but it did for me at least.