Hmm, on the desktop this didn't seem to happen. I think that was because it noticed the person creating the channel shutdown. I could experiment with explicitly closing the channel to see if that closes the dialog. Otherwise there isn't much I can do.
Message? As in using this command not just for debug stuff? I'm bypassing things a bit so I wouldn't expect the UI to work correctly.
I've heard general reports of aliases being wrong but have not ever found the cause if it is even TORs fault. I wonder if it is that.