Application of Deposit exceeds Invoice amount

Good Afternoon:

When I invoiced a customer yesterday for Invoice 2 of 3.  The system required me to use more of the Deposited funds than was shown as the Invoice total...why?  Where are those funds now?  In the Accounts Receivable screen for this customer the proper deposited balance is still reflected.  However, when I go to do the actual Invoice, the available credit balance is short by the $900.  Where are these funds?  Has anyone experienced this situation?  I am wondering if there is some type of ghost cost that was assessed on invoice #2 that isn't being reflected on Invoice #2.