Thank you for the reply Ashley H.  Unfortunately, we are going in circles here.  The article you referred me to states: "QuickBooks uses the class you add on an invoice to classify the customer payment and the deposit.  So, if you enter a payment without an invoice (or a prepayment), QuickBooks can’t classify the payment and deposit amounts. It shows as unclassified on Balance Sheet by Class report."

The payment is not a pre-payment, QuickBooks did not classify the customer payment even though the payment I entered is applied to an invoice with a class.

Here's another article that states QuickBooks rectifies issues with unclassified prepayments stating "Don’t worry, this problem is self-correcting. Later, once you apply the pre-payment to an invoice, QuickBooks classifies the payment amount correctly." 

The article mentioned above is titled  "What transactions are not supported by Balance Sheet by Class?", specifically the pre-payment, with the solution stating: "QuickBooks uses the invoice to find the correct class for customer payment. This is why you can’t add a class in the Receive Payments window. So when you record a pre-payment, it shows as unclassified on both accrual and cash basis Balance Sheet by Class.  - What you should do  -  Don’t worry, this problem is self-correcting. Later, once you apply the pre-payment to an invoice, QuickBooks classifies the payment amount correctly."

This article is addressing the issue to correct the payments that are not showing up on the Balance Sheet by Class.

QuickBooks claims it is classifying the payment amount correctly, ie. giving the payment the same class as the invoice then there shouldn't be an issue for the engineers to add the class field to the payment, making it equal to the invoice it is applied to.  This way, the reports will show the balances correctly when they filter transactions by class.  Currently, the reports are not intelligent enough to seek out the payments that are tied to the invoices.