Debit memo not being picked up by payment process even when there are invoices as well

We have a few cases where a vendor has some invoices plus some debits, and when totaled up we owe the vendor money.   But when we run the payment, it picks up only the invoices and not the debit memos.   What would make this happen?

For example: you have invoice1 for 100, invoice2 for 400, and debitD for --300.   You run payments and it generates a payment of 500 , which is the sum of only the invoices , instead of 200 which is the sum of all the transactions.  

All the transactions are validated

All the transactions are accounted

No transaction is on hold

The payment due date on all transactions has come