There is a link in this Guide that will tell you the current version:
Your version is a little behind, but no changes have been made that would affect your problem. As @Brucanna told you, the automatic application of a credit means that at some point that customer’s subaccount under Accounts receivable reflected an overpayment by the customer. That could be for as simple a reason as the customer paying off a later invoice for a greater amount than an earlier invoice for a lesser amount. So verify the dates on all sales invoices and Receive money transactions.
While I was writing the foregoing, you posted your screen shot. It looks like this customer has only had one sales invoice. So I am puzzled by your statement that “the balance always goes to $0 as they pay the exact amount each time.” I suspect your problem is that you accidentally selected the wrong customer on some other transaction. So check the history of your other customers to see if an invoice you thought was paid off still has a balance due.
This does not look like a problem with Manager, but a simple data entry error. Unfortunately, those are sometimes hard to track down.