Hey Nick,
I just looked in the code and tried to see what could be happening, but all I can see is "too much to judge". So, for all the XTweaks settings the data is obtained which is a lot of stuff that just "does" something like adding an Album to a Gallery does quite a few things (meaning : as unrelated, but many things happen anyway).
What you could try for fun is opening a Command Prompt with Administrator Rights (Run as Administrator - and Exit when it's there) because those kind of things happen in there too, and possibly it changes some general higher level things which imply a SQ difference ?
But I'd say this really is a too long shot because this (Command Prompt etc.) happens at the start of Playback as well, although not always ... (you can see the Dos Boxes popping by after a boot session ... until they stay away at some stage ... hmm ...).
Maybe somewhat more to the point is that these specific activities needs certain Services to be running, so they are started. But, they are stopped as well when Playback starts, though in the main time they may leave something behind (to die out etc.). But this would actually be counter productive to the better sound.
Meanwhile, looking into that code it reminded me that I never "set" anything for this Time Stability as well as the Time Performance Index in my new W8.1.
So, Not Stable and Note the Best respectively, and now I have this coherent sound ?
Peter