The reason that is happening is because the query for new messages isn't specifying only "domain_wide" messages, so it gets those direct ones also. If you build a 1-1 client, you'd grab history by grabbing the latest messages just from userA to userB, or from userB to userA. If your chat client doesn't grab the history of your conversation, this won't be a problem.
Currently this doesnt quite work yet because we haven't implemented the right search to return messages from/to a certain user. Are you making a chat client that would use history like this? If so I will push up the priority of implementing this.
- Brian