Do you have an example of a page with this. I browsed your site but was unable to locate a page where this is happening. I also looked through your CSS and the positioning is relative so the footer should appear after all the divs before it so I don't believe that is an issue.
Yeah, you'll need to tell us which page has a problem. But a few other tips...
Be sure you optimize your images for the web. You have a few that are really large and you are using html to resize them. Resize them in your graphic app instead. Also, your Useful Links section text doesn't work well. Any time you try to align text over a background image like this you run into trouble when visitors have their text sized differently than you expect.
Thanks for note on the text size.
It was happening on most pages, but I hadnt cleared my cache since a system crash, seems to be ok now!