I have a similar issue. Mine is even when people pay an invoice online through quickbooks itself. NONE of my deposits match automatically. The client pays online quickbooks deposits the funds into my bank account several days later but the transactions don't automatically match and this is actually done through QB and their payment system. If I bank a check after receipting it in quickbooks then it never matches QB then asks me several days later to review and match manually. I have hundreds of clients also its impossible to know what deposited funds belong to which QB receipt. So now I have hundreds of bank deposits sitting in my qb account that would take forever (If possible to match). Why does QB not match deposits to payments and invoices this is weird.