ACR MLG TRACK HDG DEV USING RNAV WITH ACFT COUPLED TO OMEGA. THE WRONG LAT HAD BEEN INSERTED AND NOT VERIFIED BY THE OTHER CREW MEMBER.

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WHILE FLYING ON THE SID OUT OF SAN JOSE WE WERE ON COURSE TOWARDS LINDEN VOR. WE WERE CLRED DIRECT (RNAV) TO A VOR 2 LEGS DOWN ON OUR FLT PLAN. WE WERE CRUISING AT FL270. THE CAPT ENGAGED THE OMEGA TO THE AUTOPLT AND THE ACFT BEGAN A R TURN FURTHER THAN ANTICIPATED. THE OMEGA WAS DISCONNECTED AND THE NAV POINT BEING FLOWN TO WAS RECHKED. WE DISCOVERED AN ERROR IN THE LAT/LONGS ENTERED FOR THE NAV POINT. PRIOR TO THIS THE CAPT FLEW THE ACFT TO HDG THAT WE CONSIDERED CLOSE TO A DIRECT HDG TO THE NAV POINT. WE THEN ENTERED THE CORRECT COORDINATES FOR THE NAV POINT AND REENGAGED THE OMEGA TO THE AUTOPLT. THE ACFT AGAIN BEGAN A TURN TO HDG WE CONSIDERED INACCURATE. THE CAPT DISCONNECTED THE OMEGA AND WE AGAIN RECHKED THE NAV POINT COORDINATES. WE DISCOVERED THE CORRECTION HAD NOT BEEN ACCEPTED BY THE OMEGA. AT THIS TIME WE ADVISED ATC OF NAVIGATIONAL PROBLEM AND ATC PROVIDED A VECTOR. ADDITIONALLY; I HAD NOTICED A TARGET ON THE TCAS SCOPE MOVING TOWARD US. THIS TARGET TRIGGERED A TA AND THEN AN RA WHICH TOLD US TO DSND. I DO NOT RECALL US TAKING ANY ACTION MAINLY BECAUSE WE HAD VISUALLY PICKED UP THE ACFT COALT WITH US AND OPPOSITE DIRECTION HOWEVER; IT WAS PASSING 4-5 NM TO THE S OF US. AFTER THE RA; ATC ASKED US IF WE HAD THE TFC IN SIGHT AND WE ACKNOWLEDGED WE DID.