The "Transcode Now" operation is transcoding of assets for timelines. And they still must be muxed with the audio during the build. There is other transcoding during the build (I think that is what it is still called when the build renders out menus/motion menus).
The "Rebuilding Audio Tracks" is what has been seen when Encore, for whatever reason, decides it can't pass through 5.1 sound. Is your audio 5.1?