Here are other items to consider with Partner Billing Rules:
Marketplace: The platform does not consider Marketplace costs when processing Partner Billing Rules or Custom Price Books.
Older Billing Rules: Billing Rules are applied in the order of first created. Check if there are multiple billing rules targeting the month and tenant in question and apply older billing rules first: https://apps.cloudhealthtech.com/partner_billing_rules
Partner Assigned Credits: Assigned credits are applied to Usage prior to billing rule calculations. Check the Partner Credit Pinning tool if there are credits assigned to the month in question: https://apps.cloudhealthtech.com/msp/aws_credit/pinning