Payment Proposal issue - Sage X3 PU9

We are a management services company managing around forty non-related entities.

Invoices rendered by the umbrella company to the customer-entities are auto-posted in the customer's Purchasing module, via a customised inter-company process, however, credits are processed manually through the AP/AR module.

My problem is two-fold : -

On the Payment Proposal, Sage segregates the 'Purchase module' invoices from the invoices/credits processed through AP/AR, and lists them separately, as though they were from two different suppliers, even though they all refer to the sames supplier.

Furthermore, Sage will not include a credit posted through AP/AR against invoice/s processed through the Purchase module, even though the invoice value exceeds that of the credit/s.

I have been through the checklist posted elsewhere on this site but I cannot fathom why this is happening.

Any suggestions would be appreciated.