Can you show a screenshot of the PO change log, maybe there were other changes made along with setting the delivery complete indicator.
I assume that you had already a GR when you set delivery complete indicator. If you look at Q&A 34 in OSS note 456691 - FAQ: Price determination in purchasing
then you can see that SAP explains that there can't be any changes for the delivery costs in conditions.
This leads me then to the assumption that there might be a custom logic which overrules the SAP logic.
Are you setting the DCI in ME22N manually, or do you use a BAPI or any other method?