Have you checked invoices from that customer to make sure they have all been paid (Make sure there is a payment for each invoice) and that all payments together do bring the account down to 0 balance. To help you better you will need to share some screenshots but I think it would be best for you to contact NCH technical team and share a backup of your data for them to review with you and help you figure out if it is a program issue or an accounting issue.
https://www.nch.com.au/support/index.html