We need more info.  Aging, Statement and Pick to apply payment - what are the entries?

Quote from JereC on 02/19/14 at 10:10:54:

 
Why - what happened?  
 
Other than that, everything sounds normal. You will have to re-enter the $20 voucher. You should be able to just say Yes to "Apply all open credits?" and "Apply to all open invoices starting with the oldest?".

Is the Deposit attached to a SO? If so, I don't believe you will be able to use it to "pay" a voucher in AR-C. You will have to delete the SO number on that Deposit in AR-N. If that's not it there are a couple other potential issues.
 
When you go into AR-C, there is a display at the lower right side of the screen that shows total Credits, Deposits and Invoices. Do you see the $360 credit there? If so, I suspect that it got entered with a bad date, as you are not allowed to select credits/invoices of a later date than the "payment" being entered. Take a closer look at the Aging Report and note the date of the Deposit. Then advance the date of the "payment" to equal the Deposit date.
 
If the Deposit is not showing up on the AR-C screen then there is almost certainly some kind of problem with the database - maybe the original reconciliation got interrupted somehow and only part of the transaction got posted. If that's the case it's quite a bit more complicated and I don't feel competent to provide support remotely. It's hard enough sitting at the machine... I would suggest using IS Tech Support. If you're not a subscriber I believe they still provide per incident support.
 
Good luck.