Hi there, I posted about this in the Topic called, "Apply Payments to Invoice." I had the same problem as you. It was applying payments as partial payments instead of to the correct invoice. It was even passing over older invoices and applying to newer ones. I had tech support helping me on this but was still unable to get it to work. Then:
Okay. I don't know why this worked and I'm not sure yet which is the "magic" step. But here's what I did:
Go to the payment screen.
Enter the payment information in the upper boxes.
Double click on the amount applied in the large box for applying a payment to a certain invoice. Put in the correct amount. Zero out the others or put in the appropriate amounts.
I've done those steps before. Here comes the weird part - and remember I don't know which is the ticket:
Uncheck the "Show Paid Invoices" box.
Recheck the "Show Paid Invoices" box.
Double click on the line of the invoice you want to pay.
Double click on the "Apply Payment to Invoice" bar.
Click on Record payment.
I successfully entered 3 payments for one customer this way and it's still showing a previous invoice as unpaid, which is accurate. YES!! Phew.
Hope this helps you!