For a PO to disappear from the PO Clearing report, the Qty Ordered must equal the Qty Received which must equal the Qty Invoiced.  You also need to have the QTY back ordered to be zero.  There is a setting in PO options that allows you to change the back ordered amount to zero if the quantity received is within a certain percentage of equaling the full quantity ordered.  For example, if you ordered 500 but only received 497, it would make the quantity back ordered 0 rather than 3.  However, the rest of the quantities must be exact for the PO to flow all the way through the process and disappear from the PO Clearing report.  I hope that helps!