Pre-payment, apply doc dates

We have been using Prepayments, and then Apply docs to keep track of deposits. However, we have recently discovered that as soon as the payment gets applied, it gets changed retroactively into a regular payment from the original payment date. So now, on the original payment date, its not showing a prepayment, but rather a negative AP. 

Is there anyway to keep it as a prepayment until the AP doc date? Is this a dating issue? Or Sage is incapable of having it as a prepayment at all once it switches?