Wow... so all it took was one person to mention it? Good job Zedrik!
I've noticed the absence in Dvergeheim, the mountain areas, the southern farmlands, the vamp lair and the purple mist dungeon, the outskirts, the Blue Water, the shore by Megan's shop, Megan's shop itself, Degannwy and Gilos' monastery. (I'm not obsessive, I just like those particular tunes
) It just seems like all the custom music has vanished.