What is it in the footer that is on top? A Flash movie or something?
I would look at fixing the thing that is on top, like with a Flash movie there is a parameter to make it windowless. You'd have to do some googling to find out how to do that as I'm no Flash guru.
I suspect you are having this problem in IE and it doesn't happen in other browsers.
One thing you could try that may help a little is:
1. Add this to the top of your theme.skin file:
<%@ Register Namespace="AjaxControlToolkit" Assembly="AjaxControlToolkit" TagPrefix="ajaxToolkit" %>
2. a little further down add this:
Valid options are TopRight, TopLeft, BottomRight, BottomLeft, Left, Right, but it really just controls the position in relation to the textbox.
Hope that helps,