I followed your instructions to the letter: uninstalled Path Finder using AppCleaner but the problem reappeared. And more: anything I open (say, a new browser) makes the main window go dim and the new window is placed behind the actual one. The only way to accede to it is by minimising the top window. Trying to make the new window come to the front through the Window menu only makes the main one go dim again.
I think this started to happen after the latest update.