FLC FAILED TO REPROGRAM THE FMS FOR THE NEWLY ASSIGNED ALT RESULTING IN A TCASII RA AND LOSS OF STANDARD SEPARATION.

Narrative

FLYING FROM DCA TO DTW ON AN ATC ISSUED TSTM AVOIDANCE ROUTING (LDN J-134 FLM D DQN MIZAR STAR). NEAR EKN WE RECEIVED A MORE DIRECT RERTE FROM ATC (DIRECT GEFFS J-149 J-85 DJB CETUS 2 STAR). ABOUT THE SAME TIME WE ALSO RECEIVED A CLB CLRNC FROM FL310 TO FL390. (OUR FILED ALT WAS FL350.) THE FO WAS BUSY FINDING AND LOADING THE RERTE IN THE FMC. I BEGAN THE CLB BY SELECTING 39000 FT N THE ALT SELECT WINDOW AND SELECTING VNAV. CLBING AND NEARING GEFFS THE REMAINDER OF THE RERTE HAD NOT YET BEEN LOADED. I DIRECTED MY ATTN TO SEEING IF I COULD ASSIST IN THIS PROCESS TO ASSURE A SMOOTH CONTINUATION TO THE COURSE BEYOND GEFFS. (SOME TYPES OF ROUTINGS ARE MORE PROBLEMATIC TO LOAD THAN OTHERS. IN THIS INSTANCE; DESCRIBING/DEFINING TO THE FMC THE TRANSITION FROM J-149 TO J-85 WITH NO INTERVENING FIX WAS LESS THAN ROUTINE. THE FO HAD THE JOB WELL IN HAND; IT JUST TOOK TIME.) ABOUT THIS TIME 2 EVENTS OCCURRED: 1) THE ACFT LEVELED AT FL350. I REALIZED THAT THE CRUISE ALT IN THE FMC HAD NOT BEEN CHANGED FROM THE FILED ALT OF FL350 TO THE CLRNC ALT OF FL390 BECAUSE THE FMC WAS BEING LOADED WITH THE RERTE. I BEGAN TO RECTIFY THIS TO RESUME THE CLB WHEN 2) THE TCASII WENT OFF WITH AN IMMEDIATE RA INDICATING A 2000 FPM DSCNT COMMAND. AS I GRABBED THE YOKE TO DISCONNECT THE AUTOPLT AND COMPLY WITH THE RA. I SAW TFC AT ABOUT 3 MI; MOVING LATERALLY R TO L. MY IMMEDIATE ASSESSMENT WAS THAT THE TFC WAS NOT A FACTOR AND I ELECTED NOT TO FOLLOW THE TCASII. IN A FEW SECONDS THE TCASII INDICATED THE CONFLICT TO BE RESOLVED AND WE CONTINUED TO FL390. ATC ACTED TO RESOLVE THE CONFLICT BY ISSUING HDG CHANGES. I OFFERED SOME ASSURANCE TO THEM AND THE TFC BY LETTING THEM KNOW I HAD THE TFC IN SIGHT AND THE LATERAL SEPARATION DID NOT SEEM CRITICALLY CLOSE. THE REST OF THE FLT WAS ROUTINE. I DON'T KNOW IF THE TFC CONFLICT COULD BE PRIMARILY CATEGORIZED AS A LATERAL SEPARATION ERROR OR A VERT ONE. IT IS UNFORTUNATE THAT OUR CLB TO FL390 WAS INTERRUPTED. CERTAINLY A SMOOTH CLB WOULD HAVE IMPROVED THE PICTURE. HOWEVER; I DO NOT BELIEVE IT WOULD HAVE GOTTEN US TO FL370; THE NEXT ALT OUT OF CONFLICT; BEFORE WE ENCOUNTERED THE TFC. SINCE THE INCIDENT I HAVE SECOND- GUESSED MYSELF QUITE A BIT ABOUT NOT FOLLOWING THE TCASII RA. THIS IS CONTRARY TO OUR TRAINING AND COMPANY POLICY. YET IN THE INSTANT THE JUDGEMENT WAS MADE; I WAS CONFIDENT AND THE RESULTS BORE OUT ITS VALIDITY. COCKPIT RESOURCE MGMNT IS SOMETIMES A CHALLENGE. IN THIS CASE I INITIALLY MADE THE DECISION TO LET THE FO WORK OUT THE RERTE PROB HIMSELF SO THAT BOTH OF US WOULD NOT BE DISTRACTED AT ONCE. YET HIS INVOLVEMENT IN THIS PRECLUDED A STANDARD ALT CHANGE TO BE MADE AND ULTIMATELY I HAD NO CHOICE; IT SEEMED; BUT TO BECOME INVOLVED WITH BOTH PROBS. OFTEN DESPITE YOUR BEST EFFORT; 2 PLTS AND A COMPUTER DO NOT MAKE FOR AN EFFICIENT COCKPIT; AND I HAVE BEEN FLYING THIS TYPE OF ACFT FOR OVER 6 YRS.