I think I have nailed this down to an issue where the processing time for Paypal is so long that every once in awhile someone will navigate away from the page, come back, and resubmit, before Paypal sends back the confirmation.

As a result, the cart isn't cleared and the customer is able to place a duplicate order.

Paypal says they can't speed up processing, so I'm wondering how I could change the 'submitonce()' functionality on the checkout_confirmation button to be a page overlay instead of just a button overlay.

There are a number of examples online, and this functionality is used in the Numinix Fast and Easy Checkout with Ajax module, but I'm trying to figure out a way to apply it to the standard template.

Any help would be appreciated.