That was changed in 6.3 or 6.31. Now, it will always highlight even the $active window if new text appears when mIRC's not the app in focus. Some people like this, others don't. It's meant to show that there was something new in the active window if mIRC wasn't the active app. In some ways this can be helpful -- a quick look back at it after having something open over it will show there is more text in case you don't remember what was said last. In some ways it isn't -- more often than not, it seems that you have another app only partially covering mIRC so that you know if something is typed in the active window, so there isn't any need for it (or you have the scripts editor open which I personally don't maximize, so again there isn't any need for it).
In any case, it isn't a bug and I don't think it will be changed. There hasn't been much complaint over it here and I think the only way it would change is if enough people didn't like it.
