Do you have a link where I can check on this. I would like to see the result that is occurring on the live page and compare this to what I'm seeing on the page that is posted here.
There is code on the checkout page to redirect you to the cart page if the cart is empty, so it would seem that something is clearing the cart out. Do you have any problems on this site with session variables? The cart relies on session variables to retain items, if there is a problem occurring with the session it can clear the cart.