That is just a setting. You should still be able to manually join a channel using: /join #channelname
I can't remember where the setting is to make the channel window appear again, but if you delete your mIRC.ini file while mIRC is closed and then open mIRC, it will create a new mIRC.ini file that should have that enabled. You'll just need to redo your mIRC options.
Or perhaps someone else knows where that setting is. I know there's a checkbox ON that dialog, but I don't know where else it is.