Same issues with my MacBook Pro Retina mid-2012. Since I'm still under Apple care, I've had it in several times to try to find the issue. They replaced the logic board, monitor, and a few other things. Still has the same issue. When it happens, I can do a restart, and it will work for a while. But when in the middle of teaching a class and want to show a short clip, this is not practical. My sound works fine when using audio on iBooks. Same sound whether using external speakers, headphone, or only internal speakers.
As others have stated, the Apple Genius, as well as online support act like they have never heard of this issue. I need to get resolved before my support runs out in June.
I glanced through this long stream of posts. Anyone have any resuts?