Why would Blu-ray made with Encore CS6 be silent/have missing audio, no sound?
The only thing I can think of is that the audio channel may not be getting set on the timeline for some reason.  I would verify what audio track is associated by default with the timeline as a first step and try a simple case of a disk that immediately plays the timeline with the audio set to the default audio track.  If that still doesn't work, I'm out of ideas.  Your situation seems very odd.  Have you tried playing it in a stand alone bluray player by any chance?