You must be using Paypal Standard.
With paypal standard, it is not a real time checkout system
to mark purchases based on the result of the transaction with the credit card company, you would need to set up an IPN page:
I dont recommend using Paypal standard because of this, in actual fact paypal standard is no longer supported in cart 6. I would recommend using Express Checkout instead express checkout is the same work flow for the website visitor, but it is a real time checkout, and will store orders only when processed through the CC company.
with eCart 5, you would need to run the checkout wizard for PayPal Payments pro, then remove the checkout form from the checkout page leaving only the checkout with paypal button.