Hi Desiree, we used to play a sound.wav when the agent received a push notification on their mobile device. I remember that we copied these sounds into the phonegap package to be able to play them. In our example we created a folder called sounds in the www folder of the phonegap package and placed all .wav files in there.
The theme folder is accessible by the webapp using a web browser. The hybrid app has it's own web app or www root folder in the phonegap package itself. So my guess is that relative URL's point to the root of the phonegap package, instead of your web app root. hope this makes sense. See also this picture.