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When I type /cs HELP it goes out like a global message to the channels, which never have happened before. Is there something I can do to prevent this, and just get it up in the status window as it always have done
This i believe is your client seeing ChanServ being in the same channel as you and so displaying notice messages from ChanServ to you in the channel and not in the status. If you leave every channel that both you and ChanServ are in and join one which ChanServ is not in the notices will go to your status window.
Just so you know they arnt actually sent to everyone, they're only sent to you. It's just a case of your IRC client chosing to display them in the channel window instead.