When the Always Highlight setting in mIRC Options -> Display is disabled mIRC is supposed to only highlight windows if it thinks they are not "visible". It appears this check is rather primitive though, because if one window is covering another then the covered window will not get highlighted. When MDI windows are maximised highlighting seems inconsistent: it appears minimized windows are always highlighted properly while results vary for windows in a "normal" state.
Steps to reproduce on a clean install (6.35/7.08):
1) Disable "Always highlight" in mIRC Options -> Display
2) Connect to an IRC server and maximize the status window
3) Type //query $me test
4) Switch back to the status window by clicking its switchbar button
5) Type //msg $me test
The second message will be received but the switchbar/treebar entries for the query window will not be highlighted.