a quick question

It stops? I know there's a little pause while the alert plays...

Maybe setting your alerts to silent while you're listening to music?
 
This is also happening to me. When listening to music and I get a txt music drops out for a moment and comes back. Sometimes while listening to Pandora the program hangs and I have to close Pandora and re-start.
 
I don't think there's a way to stop it from happening. The audio codec is probably only capable of a single output, so when notifier sends a sound, it overrides the current audio to play the alert.
 
I guess you could always stop your notifications. You would just have to manually check to see if you got anything.