I believe i have found my own answer. Credit Invoices were randomly being applied to any invoice that was awaiting payment for the vendor. As we have several Classes, I have to inform my staff to only apply a Credit Invoice against a same Class invoice for that vendor.

Corrected by the following

DR Correct Bank Account and Class

CR Incorrect Bank Account and Class

Just a note for anyone else who has class issues:

• Unpaid Bills report does pull in credits when exporting the report for check run balancing prior to making payments. it is very useful to know whether you have included all credits you intended.
• Check Detail Report Displays Net paid (includes credit amounts) but does NOT include the Credit itself on the detail unless you manipulate. If you take the difference between the Check Paid Amount and the Original Amount, that is usually our credit amount.