With the LinkTree positioned at the top of the browser window and then turning on or turning off a Core feature you will see the LinkTree bleed thru the confirmation bar.
Position the search field in the header to the top of the browser window and there is no opacity when the confirmation bar drops down over the search name and input box.
Is the confirmation bar drop down even needed? Seems the CF icon going green would be enough feedback to the admin.
ETA: Browser is FF 28
Small z-index issue, good catch, fixed here: https://github.com/Spuds/Elkarte/commit/7b25e1daecc63b76754d4bd09d52b1a869781dc5
Yeah its probably excess as well, the changing of the icon is probably enough.