I’ve only noticed the problem when playing M4V files. This is in both iTunes 11.1 (Released version) and Quicktime. In iTunes, I have discovered that the problem only exhibits itself when playing back in Fullscreen. If I take the video out of fullscreen mode, the audio plays fine.
VLC can play the videos fine in Fullscreen mode.
I am playing the audio through the builtin speakers on a MacBook Pro.