I tried the new "Accept Deposits on Sales Order and Invoice Flows" feature in 2012.1, and was initially excited when I took a deposit from a button in a sales order. After I chased down why the customer had $30 showing up on our A/R aging report I was much less enthused.

The problem is there is no opportunity to enter a discount in the deposit or payment screens of this new flow. My prepayment via international wire was short $30 due to intermediate banks (virtually all our prepayments are via international wire and most of these wires are short roughly $20-$35 due to these bank fees). Thus, my sales order was entered as $X, but the deposit was entered as $X-30, so when the deposit automatically applied to the invoice it left a $30 balance open on the invoice. I'll have to clean this up with a journal. Grrrr.... it would