Providing an update here. I talked with a tech support person on the phone, and the problem was not duplicate records. The problem was the Deposit field as displayed in my screenshot above. There were no duplicate transactions. The Deposit field is not treated as a "deposit partial payment of the invoice", rather it is deducted from the total invoice amount as if it were paid prior to the invoice being sent by other means (e.g. check/cash). Removing the $250 from the Deposit field updated the Balance Due to be correct, which was $250. Just providing this solution here in case other people are using the Deposit field incorrectly, as shown in the image above.