I had an issue once with sound that is now fixed. My game was set up in the following way
Logo Splash
-Music is preloaded
Title Page
-Music begins at start of layout and loops
Levels
-Music is allowed to continue to loop unless the "EXIT" menu option was chosen at the end of the stage. I had an event that ended the music before heading back to the Logo Splash layout.
What ended up happening was that the music would cut out randomly in between the levels depending on how quickly the user selected the menu items. It was almost as if the events got tangled somehow.
In order to fix this I had to move the "music stop looping" event to the beginning of the Logo Splash, so that when a player selected "EXIT" and returned to the Logo Splash layout, it would stop the music then and not effect the sound in between levels.
Not sure if this at all has anything to do with what is going on with your project, but just wanted to show you that you may just have to mix up your events in a different manner to get the end result.
-Mike