Did you post these receipts as a 'Delivery note'? This would account for the fact that the invoices are not in Payables.

In POA go to Process\Reports and print the 'Outstanding receipt invoice list'. If you find your missing transactions on this report then you need to use the Inv/Adjust/Rtrns function to convert the Delivery notes to Invoices. Next Day end will then flush them out to Payables and create the offsetting entry to your clearing account.