A recent change to the Blogroll widget may have broken your custom css.
<ul> now carries the class "xoxo blogroll". The problem is that many people use the identifier "ul.xoxo" in their CSS to apply style to their widgets. So you may find that your blogroll is suddenly out of whack somehow.
All you need to do is create a more specific rule for your blogroll which nullifies earlier rules. You could use the identifier "ul.xoxo.blogroll" to specify the rules.