Did the radio stop intermittently or did it stop entirely?
I know that when "the nav gal" is giving you directions, the radio will cut out temporarily so that you can hear/understand what she says with no other interference. It is only for a couple of seconds and then whatever device you're listening to (radio, CD, USB, etc.) resumes.
I don't recall if it cuts out when giving a nav command (setting up a destination), but I would assume that it would so that the computer can understand exactly what I'm trying to say without any background interference that might cause it to misunderstand my commands. Again, I would think that the music would cut out only as long as it takes you to finish your command(s).