We have a misc item with a  GL account for OVER/UNDER shipment or invoice value differences - we add that line to the PO - receive it in and this completes our purchase order. The OVER/UNDER GL account is monitored at that point.

A PO line being invoiced for a different cost than what was on the PO when you received it will not prevent the PO from moving to a complete status.  That just generates a price variance and the software will post that variance and move on.  

For a PO to move into a complete status, each inventory item and misc item line on the PO has to meet the following conditions:

Quantity Received<>0

Quantity Invoiced=Quantity Received

Quantity Backordered=0

If your PO is stuck in a Backorder status, it won't be because of pricing variances, but most likely is due to one of these conditions not being met on one of the PO lines.