It feels like the problem (at least for me) where introduced when I went from OSX Lion to Mountin Lion. I have also tried Movist and MplayerX but these does not show the sound problem (but in these cases the picture quality in not as good as the VLC), therefor I'm very anxious to have VLC player working again Prior upgrading to OSX 10.8.0 the sound worked fine with the same HDW setup, and the sound output set to HDMI. I have also tried both 2.0.3 (stable) and the pre-release - 2.0.4, none which correting the problem. I have in a manner of troubleshooting, downgraded to 2.0 without any impovement. 2.0.1, and efter I upgraded OSX to version 10.8.0.
This happens when I have the sound output within VLC player to 'HDMI', when I change it to 'HDMI Coded' it will be corrected, though, I will now longer have the real power in the speaker, and the sub are almost inactive. Music and background sound are coming from both speaker, though, with a slight more to the left speaker. When I play a mkv-file, which normally has DTS encoded sound, the speech are directed to my left speaker. I have a mid-2010 Mac Mini, which is connected to my LG 2.1 reciever through a HDMI cable. I'm actually having the same problem, but with a different setup.