Authorization Capture With Anet

I have started to run into a problem. We use authorization only with AuthNet for initial order payment. Once we process the order and shipping charges, we change the payment method to another AuthNet we set up that will capture the charge instead of just authorizing it(same merchant account, same authnet account, same credentials). There use to be no problem with this but now when we capture the card, the original authorization transaction is not captured, a new transaction is created for the capture instead and this transaction is what settles. This is causing a list of auth only transactions to remain active after settlement instead of being converted to a capture.

Was there a change to a process during the last upgrade? Or am I missing a new setting?