Do not edit the Twenty Eleven theme. It is the default WordPress theme and having access to an unedited version of the theme is vital when dealing with a range of site issues. First create a child theme for your changes.
As esmi said, create a child theme so that you can fallback on the parent if there is a problem. I would check the code for these template files over. It looks like you are loading your entire site in an iFrame inside of the section where the second navigation bar is showing.
Also try disabling your plugins, it seems like the problem may be coming from a slideshow plugin.
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