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    So, I just replace the catalog.xml and that didn't do anything. As an experiment, I added a new product with NO custom options and made it a related product for another item, and the checkbox showed up for that item. So, it was like I thought, the checkbox will not appear if you have custom options as there's no way to add items to your shopping cart with custom options. You must first go into the product and configure the options and then add it to your cart.