HDG TRACK DEV AND POTENTIAL CONFLICT DURING THE SELBY ONE DEP PROC BY A B738 FLT CREW WHEN THE RTE IN THE FMC IS NOT THE SAME AS THE PDC WHILE ON FREQ WITH N90; NY.

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ON DEP; WE MISSED A WAYPOINT ON THE CLBOUT. THE FMC AUTOMATICALLY LOADED ITS OWN RTE. I VERIFIED THE RTE WITH THE PDC AND THEN WENT TO PREFLT. THE CAPT HAD YET TO ARRIVE WHEN I LEFT. WHEN I RETURNED; HE WAS PROCEEDING WITH HIS SETUP. HE CHOSE TO FLY FIRST. WE DEPARTED USING LNAV TO FLY THE DEP. WHILE LEVELED AT 6000 FT; WE RECEIVED A TCASII 'TFC' ALERT. THE CTLR ADVISED US OF THE TFC WHICH WE HAD IN SIGHT. HE THEN ASKED US IF WE WERE ON A HDG AND WE TOLD HIM THAT WE WERE FLYING THE DEP. THE CAPT RECHKED HIS MANUAL AND FOUND OUT THAT 2 WAYPOINTS WERE MISSING FROM THE FMC. WE QUICKLY RELOADED THE FMC AND GOT OVER TO OUR RTE. NOTHING MORE WAS SAID TO ATC. WHAT I FOUND OUT LATER WAS THE CAPT WAS SUFFERING FROM SEASONAL ALLERGIES. HE TOLD ME HE WAS OUT OF MEDICATION TO TREAT THEM. ALSO; HE HAD A TOOTH PULLED A WK AGO AND THE SOCKET BECAME INFECTED. HE CALLED IN SICK FOR A TRIP PRIOR TO OUR PAIRING; BUT BECAUSE OF SCHEDULING'S MENTALITY ON SICK CALLS; HE WAS AFRAID TO CALL IN SICK AGAIN FOR FEAR OF RETALIATION. HE ALSO LATER TOLD ME HE GOT INTO THE COCKPIT AND RELOADED THE DEP MANUALLY WHILE I WAS OUT PREFLTING. THIS CAPT WAS NOT THINKING CLRLY AND HAD NO BUSINESS FLYING AIRPLANES IN HIS CONDITION.