I'm having the same problem with my Pro 2019 version...followed your advice to use the "Print and PDF Repair Tool" but that didn't solve the problem which is:

1) I receive a payment and the invoice properly shows that it is paid.

2) But when I print it to paper or PDF, it still shows the full amount Due

So it shows differently on the screen than when printed. I am trying to send a customer an accurate Amount Due invoice for which he has paid half, but the PDF invoice still shows the full amount.

For your added information, when I create an invoice and check or credit card payment at the same time, it prints properly. The problem is when I enter a  payment that comes in later using the Customers>Receive Payments tab.  

Please help.  Thank you.