I'm not entirely sure, but do you perhaps have the "On Top" setting turned on for the main mIRC window? You can turn it off by clicking on the mIRC icon on the top left of the mIRC window and clicking on "On Top" if it was checked, or by going to alt+o -> Display -> Options -> [Windows..] and unchecking "[x] mIRC main window always on top". If you disable the option, then other windows are allowed to be displayed on top of the mIRC window. If that option already was disabled, then something else is going on..