Problem is that some users having clicked on the PayPal option might change their mind. However, once they have clicked PayPal and then return to the site to choose another payment method, the items have disappeared from the site, i.e. the system assumes the transaction has gone through. Isn’t there some marker that PayPal can send when the transaction is successful? As opposed to the products dropping off as soon as they select PayPal?
I too am having this issue. We had an order go through on PayPal, but never got the confirmation from Magento. When I went into the back-end, the inventory was reduced, but there was no sales history. The next sale we had jumped the invoice number. It’s like the sale never happened, yet Magento knew that something had happened. I had to manually make the sale in the back end. Something amiss with the Paypal module.