We have experienced the same issue since a program update a month or so ago. Yesterday, I ran the Quickbooks Tool Hub (Go to Program Problems/Quickbooks Program Diagnostic Tool). The payments are now matching (sort of) with the invoices, so that's a lot less work. However, we still have to make the deposit manually. Some progress, but I agree that Intuit's response to this loss of function is VERY frustrating and has me thinking of alternatives.