I have in theme
<link rel="stylesheet" type="text/css" media="all" href="<?php bloginfo( 'stylesheet_url' ); ?>" />
I had 3.6 wordpress with my own theme and plugins witch have css. Since on update changes in plugin css i made changed on plugin update then i put just what i change in theme css. Now i did wordpress 3.7.1 update and somehow now plugin css is overtaking my theme css changes.
PS maybe helps. Also Previously admin menu on beeing logged in was just showing 25px space. Now this top admin menu shows up in my theme when im logged in.