Let me help you sort this out, @sassypantsdesign.
Since you're seeing a different amount other than zero at the bottom of the Reconcile window, it is possible that there is a discrepancy on your reconciliation.
To determine the main for the discrepancy, let's pull up your Reconciliation Discrepancy report. Here's how:
On the other hand, since you're able to enter your credit card statement balance, let's make sure you're able to record the payment for your purchase separately. Use PayPal and the credit card as the payment method in paying the purchase. Once completed, you can now proceed with reconciliation process.
Keep in touch with us here in the Community if you have other questions about reconciling your PayPal transactions in QuickBooks Desktop. I'm always here to help.