Thanks for reporting these issues! It sounds like there are a few different issues here, we just need some clarifications before we investigate please.
Are you both on the same forum? If so it could be potentially related to the message move issue below, which we are discussing internally:
Also when you say notifications, do you mean the blue dot unread indicators for the channels? Where did you see the count of 54?
I am not really sure how this would have happened; the only place where threading can be enabled/disabled is this screen. Did any of your admins change any other settings there? Perhaps there is some bug where we are changing threading_enabled
when other settings are changed: