Haven't seen your template, so any healp here is sort of guessing... but since it obviously is a template problem, then it suggests something I read a while back.
The template might not be ending correctly.
If the issue seems to be gone using Firefox, but appears again in IE, this is often the problem... at least from stuff I have read.
I am NOT a programmer, so I might (probably) be mistaken here, but this problem can be caused by open tags. FF closes this automatically, whereas IE doesn't.
Check your template (footer.tpl - calculated guess) and add the following code to the bottom of the file: </div>
Might be somewhere else or something else though...
