I deactivated all of my plugins and had the same issue. Footer was even higher than before. Reactivated and now my background color and margins are off. But, once again, only on my homepage. Other pages look fine.
I have found the problem. On the child theme, ‘Check to disable Recent Posts/Content on homepage’ was checked in Theme Options->Homepage/Frontpage Options. When I unchecked that, the margins and footer returned to normal.
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