Without seeing the full HTML markup it's hard to know for sure, but it's likely that this is due to IE 6 rendering the box model in quirks mode [1]. In order to get IE 6 to use standards mode, make sure you are explicitly declaring a doctype at the beginning of your HTML page:
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
If you are using an XML doctype, make sure you are NOT starting with an XML declaration. If you have an XML declaration before the doctype header, IE 6 will fall back on quirks mode. If you are using an XML doctype, your header should look like this:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
NOT this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
[1] http://en.wikipedia.org/wiki/Quirks_mode