@4:59:00, when Y'shtola is talking to Runar... is this possibly the sound? THE Sound?
I went back to watch the 5.2 cutscene, where Urianger lost concentration and fell into the water, and you hear a very similar sound when Urianger walked on water! Moments later, Thancred has a dizzy spell, but you don't hear a sound. I think this must be deliberate; Urianger didn't lose concentration because the link between his body and soul was weakening, but because he heard the Sound! @59:20
Alisae hears the Sound too in 5.3. @40:40
In 4.5, Master Matoya's magic broomsticks just randomly stopped working. Remember, Hythlodaeus said that anything that was in range of the sound began to warp, and that the magic of the Ancient's stopped working. Makes sense; the Ancients were far stronger magicians, so their magics would have been more resistant. With broomstick magics being casted by far weaker beings, the magics could have been disrupted before people could even begin hearing the sound.
EDIT: I'm guessing that Zenos and/or Fandaniel are tied to the source of the Sound. Setting aside how already wonky Zenos seems to be, he has been described as a beast twice this patch: once by Elidibus in the solo duty (Elidibus not being able to comprehend Zenos' true nature, much like how it seems the Ancients don't really know what the Source of the Sound is all about), and again by G'raha Tia in the 5.3 ending narration. The monsters spawned by the Terminus event during the Final Days were repeatedly described as beasts as well.
Also, you have Fandaniel. His pink soul crystal records his dialogue during Zodiark's summoning, and it appears that something went very wrong. Considering how the Source of the Sound warped creation magics, I'm guessing that during the summoning of Zodiark, something went wrong and Fandaniel got screwed up somehow.