What is the DOCTYPE of the page? Also, what browser is it? I have seen this issue on pages with invalid/old DOCTYPEs with IE6-7 in Quirks mode.
In quirks mode, javascript values(like scroll position), can be off, resulting in a bad render. You should ensure you have a valid DOCTYPE that forces IE into standards mode like..
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">