I have the same problem. It must be a bug. It is working on the demo site.
The vendor deposit posts two journal transactions in a single step. First, a payment is made to the vendor and then a credit memo is generated showing the vendor owes you money (or a product). When the item is received, you post the invoice from the vendor and move to the Payment window. The credit memo and the invoice should both appear. If they are the same, check both boxes and post the bill paid (it will be a $0.00 transaction) and everything will close. If the amounts are different, the vendors account will have a remaining credit or balance owed depending on which was greater.