Nathan Craven found and fixed this issue today.

We found a bug that was introduced around April 20th that disconnected payments being made from the customer portal or app from the invoices they were intended to pay. We are in the process of fixing this now. Please note that you may have customers who have paid invoices and have zero balances who still have invoices showing as current. We will publish a workaround in our next update to describe how to fix these.