Box overhang
The box overhang is intentional. For a couple of reasons.
\r\n\r\nOne is that I can do it that way. I sort of like the effect.
\r\n\r\nThe other is that my main "content" type can be indented somewhat from the left margin, but not overly. If I had to make the content fit fully to the right of the navigation boxes, I'd be losing a lot of page space. The content text will flow under the nav boxes (you can see this currently, resize page if the effect isn't clear) if there's enough bottom-hang to it. So I get a decent bit of layout without lots of negative space.