Hi,
Please see the below notes and check if they're relevant to this issue:
76354 Information: Settlement after results analysis
338922 Analysis note for cross-company transactions (delivery)
67210 Make-to-order: Referencing and cost planning
If neither of the above notes outline your issue in detail, please let us know with a more detailed example highlighting transaction codes and screenshots and making sure that your issue belongs to a CO component?
Thanks,
Robin