Muffled voice in the back of stage?

Its possible that whoever made the recording, did a poor job. Maybe they did al1right with the musicians on the front of the stage, and messed up on the rear.

Also, disconnect one of your speakers and listen to the one that's still connected.Then do the other speaker. If one side sounds ok and the other doesn't, it will help isolate the problem.

"For instance, when I was watching Master and Commander this week, and after the opening scene the crew is speaking to each other on the deck, the camera and mic taking different angles throughout the conversation, from most angles every voice is clear, but in a few cases a voice at once gets very muffled."

You can't go by that. Even though they set up and record like you say, they generally don't use those vocal tracks. After they're done filming, the actors go in to a recording studio and record the vocal tracks again. Those are the tracks that you are listening to when you watch the movie.

I think you should isolate each component in the system and see if you can't narrow the problem down to a specific piece.