Is it the text size/appearance that is different? Perhaps the Vaadin theme’s CSS is affecting the appearance of the elements for the header and the footer.
You’ll have to use something like Firebug to find out what elements are being hit by which CSS rules, and customise your own theme to adjust for them.
There’s probably a simple global font-size property that you can use to make everything bigger (but that will then make the Vaadin bits bigger too).