It seems your question is unrelated to this thread. They are scripting to evade the behavior you're asking for, which should already be happening unless you've changed something.
By default, mirc-options/display has the box checked for "flash icons". When that box is checked, the query window in the switchbar and the treebar flashes each time a query window receives a message, otherwise it's a solid color. The color dropdown at the bottom of that same menu window controls which color the query window uses.
