At first, I thought one of the images was resized, but no; there's actually a 1px difference between them. The body's font-size is smaller than it is elsewhere and the footer-content is inheriting that. It's also got the same line-height issue that the sidebar did (which means both differences are present in the Notepad and Messages as well).
Adding both font-size: small; and line-height: initial; to the footer-content would mostly fix it, but even then there'll probably still be some little alignment issues. Might as well add line-height: initial; to #Footer, too.
