Credit Memo not being selected in Payment Process

We have a vendor with a credit memo for 18.42 and an invoice for 1048.42.  Originally, the supplier site that these are entered under was flagged to pay each document alone.  We ran a payment Process and the credit memo was not selected in the payment process even though the due date was within the parameters of the payment process.  We figured perhaps it would not pull in because of the pay alone flag as that would try to create a negative payment.  So, we unchecked the pay alone flag on the site and tried again but it is still