That's not the problem. I see this too on a 9.1 system. If I follow the instructions from larryy, the Mac plays all the output through the correct speakers, as does Quicktime, but VLC does not.
I updated to 2.1, and it's still a problem for me. The center channel seems to be sent to the rear-left speaker. I connect my mac mini to a 9.1 receiver via HDMI. The problem only happens via VLC, not when I use other media players.
I'm having the same problem, with a 7.1 output sent via HDMI to a receiver with 9.1 output (7.1, plus upper right and upper left channels). The problem doesn't happen with MPlayer or Quicktime.