There is a feature of WordPress which I consider to be a bug. I’m tempted to raise it as such with them, but I’m seeking clarification at this point.
Nonetheless, it manifests this way;
New user signs up for site. Everything goes well. Visit your new diary, the layout is all messed up. That’s because a whole bunch of default widgets have been added by WordPress, and the first widget area in Genesis is the Header Right widget. On the standard WP theme this isn’t a problem because the first widget area is laid out differently to Genesis.
In short, to fix your layout, you need to remove all the default widgets from your Header Right widget area.
I have uploaded a fix for newly created diaries from this moment forward, but unfortunately there’s no simple way to retrofix it.