The "white box" will appear in MSIE versions earlier than MSIE-8.
This is because Microsoft refused to obey (comply with) many of the standards being set for CSS.
Millions of people complained over the years and MS eventually ate humble pie and started to build their browser to incorporate the CSS standards.
The trouble is that if you apply a "code fix" that corrects the problem for MSIE, you risk messing things up for other browsers.
Before you try to correct this, you should look at the site in Firefox brower (which you should get anyway, because they have superb webmaster add-ons that make building your CSS and your site so much easier)
You can try the following to force a fix by editing tpl_header.php (in the common folder of template_default) and commenting out (around line 90 - 94)
HTML Code:
<div class="clearBoth"></div>
So you get
HTML Code:
<!-- <div class="clearBoth"></div> -->
It may work for you...
Bear in mind that later, if you want to use Banners in the header, you may need to re-activate the break.
Also, I trust you are aware of the need to place the edited tpl_header.php into your CUSTOM OVERRIDE folder. It is not a good idea to overwrite the CORE file.