Happened to me too a couple of times.
http://www.youtube.com/watch?v=yQ6vL8Nprzg&list=UUQNcXCSjmDj8CJJ2FhhqYQQ&index=1&feature=plcp
I tested it out, and when i change the audio device on GW2 the sound changes to what device I choose. It does not stop when I minimize GW2.
I also tested the audio on my speakers/headphones and it was working fine, music and youtube videos worked fine but the audio tone did not stop.