That's a symptom of using the PayPal Website Payments Standard/IPN module but PayPal is having problems telling your server about the new order. In such cases your server will never know about the order until PayPal's notification completes. There are all kinds of steps involved in troubleshooting that.
Your BEST solution is to click Remove on the PayPal Website Payments Standard module, and click Install on the PayPal Express Checkout module and set it up according to the instructions: https://www.zen-cart.com/getpaypal
If, however, you decide that you want to continue using the old "Standard" method that was never designed for database-driven shopping cart sites, you can go through all the following steps to attempt to sort out your problem. It will NOT guarantee that it will work though. Better to use Express Checkout instead.
http://www.zen-cart.com/wiki/index.php/PayPal