I see... I don't think it's about a missing setting. As no customization defines business transaction of the document; it's all core pre-defined processes in SAP. So, it's possible that behaviour has been changed or, actually, was incorrect before. Look for example at note 1737555 - Invoice with Price Difference; FM behavior changed which is not applicable for you, but states a possibility of such impact. Functionally speaking, 'RMRP' for MIRO sounds more correct. RFBU should apply for price difference, for example.
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