I have that exact same text in my .htaccess file (in the root folder of course) and replaced the 'yoursite.com' with my domain. Not really sure what else to do. It doesn't seem to matter if the zen cart is installed in a sub directory since yours works well, i.e.
www.mysite.com/shopping.
If I'm not mistaken, it seems to only have problems with the home page when first loaded. On a separate web site, I've posted direct links to specific product category pages -- when I click on those links, the page loads up and the menus drop down just fine. I'm not sure if that has to do with something else, but may be helpful in figuring this out.
I see that your test site as well as many others who have used your template don't seem to have any trouble and the menus drop down in IE6. I greatly appreciate your time and continued support with this issue.