I'm a new user to Bodhi Linu - love it! I've been fooling around with settings and could well have created this problem myself - I don't know.
All applications including the settings windows have lost the buttons that make it possible to close maximize and minimize windows. The only exceptions are Slimjet browser (which was not part of package management) and some nested settings under "settings". I"ve attached a couple of screen shots to show you this.