in tools/options/irc there are 6 checkboxes on the right side.
Can you confirm whether you have a checkbox next to showing notices in the active window?
If you uncheck that box, the notices should instead appear in the status window.
If that still happens, or wasn't the cause, try disable script handling of events to see if that stops it: /remote off
when you're done testing that, be sure to turn that back on: /remote on
