With Paypal Standard your customers are required to click a small text link that says "return to vendor site" in order for your website to receive the payment confirmation details. Unfortunately, many customers close the Paypal window after being told payment was made, which prevents your website from sending the confirmation email.
Paypal offers other premium services that prevent this issue, but they are not free, so we're working on a modification to their code to see if we can bypass this.
In the mean time, you may receive a payment confirmation from Paypal and no confirmation email. If this happens you can still login to your website to view and print the order. We've also added a page with a graphic illustration telling customers to click the "return to vendor site" link that appears when Paypal is first loading.
We will keep you posted on our progress.