When you use a boxed layout and you add a new row in the header builder the new row goes out of the boxed layout. See screencap.
Where exactly do you choose the boxed layout?
Are you talking about choosing boxed layout in Theme Options or disabling full width for row in row settings in Header Builder?
I activated the boxed layout in Theme Options. The Full Width Content has been switched off in the extra row added in the Header Builder. Result, the header flows over at the right side.
Hope this helps.
It seems like the issue is with your site only.
I tested it and it works fine for me.