You won't find it Applied, if it shows here: "why under the receive payment screen the customer still shows an available credit and I cannot find a report that will show how the credit was apllied"
Because, if this had been Applied, it would not show in that screen as Available.
"the balance sheet shows and invoice and I am able to follow it to the balnce side and it all seems correct"
Here are other things to look for:
Open your Items List and right click in the body and choose Customize Columns. Add to your view the Three accounts: Account (which is the Income side), Expense and Asset. Look for an item you linked to AR. Using that on an invoice is Self-referential and Mirror image = AR credit.
Run your AR Aging Detail report for All Dates and double-click any entry that you see for this name. Also, look at the Transaction Type on the left. For instance, someone could have posted to AR manually on the Expenses tab of a Check or Bill or Credit Card Charge entry.
