We have the same issue and customers hate it.  I just did a payment to an account for a previous invoice, and then checked the invoices we created this morning to see if it will show this new payment and it doesnt.  Quickbooks always displays the current balance on the date/time the invoice was created and doenst take into effect any payments made since.  Can quickbooks do an update that will fix this?  its not an account thing - i feel like its just a quickbooks bug