Apparently, any menu with a check mark gets offset so the menu words line up with the left of the menu title. With the check it pushes it to the left. Looks even weirder because the menus are no longer connected to the menubar for some reason. I'm really disappointed with the seemingly random changes to the UI which do nothing to help but actually DECREASE usability. The flatness and monochrome window buttons, sliders and other elements is killing me. Apple Mail which I'm in all day every day is virtually unusable just because of these UI changes.
I really hope someone will come to the rescue with a UI reface application or something to bring back color and distinction between elements.