Adding a manual payment directly to the Payments account DOES NOT help resolve the issue.

I always enter all payments manually. I receive an email from Intuit that an invoice was paid from an email and I enter that payment manually. And every time I have a partial payment - it doesn't let the customer to pay the remaining balance. It will show in the subject line that there is a balance, but when they go to "View and Pay" it says "Paid in Full". Now they can't pay the balance, which is very inconvenient for both parties (us and customers).