Just to try and get the cart page working I rebuilt that page, deleted all the checkout pages and regrenerated those checkout pages. I still get "Cart is empty" when I go to one of my Add To Cart buttons then view the cart. Is this because the product pages are suffering the same fate as the cart page and having the top php deleted by the template? I really didn't want to have to redo all those pages but it looks like I might have to.
Yep, That was it. Rebuilding the pages with the ATC buttons.