I received a second Surface 2 yesterday and the issues still remain on both devices. Steaming Flash video causes stuttering/popping and playing any audio source at volume 80 or above with audio enhancements enabled results in distortion. The audio enhancements do make the audio louder so it could just be crossing the threshold where the speakers will distort.
The distortion at high volume only occurs through the speakers, headphones sound fine. The flash problems are the same through both speakers and headphones.
To be thorough I tested the new Surface both pre and post updates.
When I had the problem it was affecting every single sound, XBOX, Youtube, Games, Video, etc and all of them were crackling, low, one speaker louder than the other.
If your problem is only happening with an specific application, then it might be the app itself, or the video source or even network.