Page footer renders incorrectly

After upgrading to Confluence 3.1, applying my old changes to the footer-content.vm and header.vm templates, the footer will render at the bottom of the browser frame or at the bottom of the page's content if it is smaller than the browser window is high. It looks like the footer still has adequate space at the very bottom of the page, the content just doesn't render there. I've also tried changing footer.vm but it has the same effect. It's also worth noting that making the footer any taller than the default causes the bottom of some pages (the dashboard is an example) to be clipped off by a few pixels. Nothing is completely covered, just partly.

After restoring the .vm files that shipped with 3.1 the problem went away on some pages, but still exists on others (despite it just using the default footer). I can't find any sort of recognizable pattern and unfortunately I can't attach any screenshots...