It's utterly ridiculous that clearly quickbooks has an issue with partial payments of invoices and every single freaking question directs people to call technical support. Perhaps you could actually fix the issue!  I have the same problem. Partial payments were made but quickbooks clearly shows $807 is still outstanding within quickbooks, but when customer clicks invoice for online payment - it shows zero balance.  FIX THE PROBLEM. I see the exact same issue for the previous 2 years!