I agree with James Huff in his prior comment, I have also use that method and it worked…completely forgot about that one! For SEO I have used and like SEO by Yoast as well as the tools available through Jetpack.
I have not had issues with Google apps, but I’ve only used that method once.
I used the method prescribed by Google of going through my web host to verify. That proved to much easier and it worked on the first try.
I’m not sure I can be of much help here, but I notice its only on the home page. It looks like the banner/links images may be doing something to much the sidebar down.
Edit: I see they are set fixed width..scratch that comment!
It could be that the sidebar element is set too wide based on the width set in the page container. Or more than likely you should look at your div for featured content.
Like I said, probably not useful but I thought I would take a stab and look at it.
