When I receive a payment and input the deposit, it goes in as undeposited funds. Having an issue when sending out invoices, where it shows in the body of the email that the balance due is xyz, but when the customer clicks on the invoice itself it shows the full invoice balance, even though they've already paid half of it. I can delete the check that I deposited in the system, delete the transaction, and then go in and manually put payment with check with the deposited amount. It'll then take that balance down, and show that a payment was made in the invoice that I send out, and will show the correct amount when I send it out.
When previous payments received are properly applied against an invoice it reduces the amount due. If you create an invoice for 1000 but customer gives you 500 and you apply it and now send out the invoice by email they should only be able to pay 500.
Quite possibly if you are not trying the deposit (down payment) to the invoice then this is what is happening