WDB CARGO JET STRAYS FROM COURSE WHEN A WAYPOINT IS NOT PROGRAMMED IN THE INS.

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RTE OF FLT WAS FROM EWR TO LAX. SCHEDULED DEP TIME WAS XA10 EDT. WE WERE ADVISED AT XA00 THAT A PDC WAS NOT AVAILABLE DUE TO A COMPUTER MALFUNCTION. AT THIS POINT; CLRNC (CPT) WAS CONTACTED; AND COMPLETE ROUTING CHANGE WAS RECEIVED. THIS MADE THE FILED ROUTING ON OUR FLT PLAN/RELEASE USELESS. AT THIS POINT WE BEGAN PROGRAMMING INS WAYPOINTS USING ENRTE CHARTS. THE NEW ROUTING WAS 'EWR 5 ELIOT ETX J80 MKC' ETC. THE INS COORDINATES WERE ENTERED BUT NOT RECHKED DUE TO TRYING TO MAKE AN ON-TIME DEP. BECAUSE OF THIS; ONE IMPORTANT FIX WAS MISSED. FROM OVER ETX J80 GOES TO KIPPI INTXN AND THEN TO AIR. I HAD J80 SET UP ON THE CDI; BUT WE WERE NAVING ON INS. AFTER PASSING ETX; I NOTICED THAT THE ACFT DID NOT TURN ON THE COURSE I HAD SET IN. I CHKED THE CHART AND THE INS WAYPOINTS AND DISCOVERED THAT KIPPI WAS NOT ENTERED. I STARTED A L TURN TO CORRECT BACK ON COURSE AT ABOUT THE SAME TIME ATC (ZNY) ADVISED US THAT W WERE 6 MI R OF COURSE AND SHOULD CORRECT TO THE L (ALREADY UNDER WAY). NEEDLESS TO SAY; IN THE FUTURE; PROPER COCKPIT SETUP PROCS WILL TAKE PRIORITY OVER TRYING TO MAKE A SCHEDULED DEP.