Thank you, that solved my problem. :-)

Code:
; Stop query windows from flashing after 20 seconds by setting them to an 'event' state.
; Ensure Options -> IRC -> Flash On Message (Query) is turned off.
ON *:OPEN:?: { 
  flash -r20 $nick
  .timer 1 20 setQueryColourToEvent $nick
}

ON *:TEXT:*:?: {
  flash -r20 $nick
  .timer 1 20 setQueryColourToEvent $nick
}

alias setQueryColourToEvent {
  if ($window($$1).sbcolor != $null && $window($$1).sbcolor != event) { 
    window -g3 $$1
  }
}