I can confirm this problem on XChat 2.8.4-0ubuntu7. If I start typing a message before all of the channels are auto-joined. The focus changes as the channels load and the message becomes splayed throughout the channels. While waiting would be an option in this case, cleaning up the splayed text and rewriting the message takes time and someone on a lot of networks may not want to wait until all of the channels are joined. Having the focus remain on the selected channel and not going to autojoined channels would fix this problem.
I can confirm this problem on XChat 2.8.4-0ubuntu7. If I start typing a message before all of the channels are auto-joined. The focus changes as the channels load and the message becomes splayed throughout the channels. While waiting would be an option in this case, cleaning up the splayed text and rewriting the message takes time and someone on a lot of networks may not want to wait until all of the channels are joined. Having the focus remain on the selected channel and not going to autojoined channels would fix this problem.