DC8 FLC OVERSHOOT ASSIGNED ALT WHILE TROUBLESHOOTING NAV PROCESSING EQUIP.

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DEPARTED FLL INTL. WAS GIVEN A HDG TO INTERCEPT THE FLL 9 DEP; THNDR TRANSITION; 16000 FT. CAPT WAS FLYING AND CALLED COURSE ALIVE. AS THE COURSE INDICATOR MOVED TOWARD THE CENTER; I BEGAN TO TURN AND INTERCEPT WHILE CLBING. I GLANCED OVER AT THE FO'S COURSE INDICATOR AND HIS WAS NOT MOVING. I BROUGHT IT TO HIS ATTN. WE NOW DID NOT KNOW WHICH INST WAS CORRECT. BOTH VORS WERE TUNED TO THE SAME FREQ. I ASKED THE FO TO CONFIRM OUR POS WITH DEP; BUT INSTEAD HE ASKED THEM IF THE VOR WAS WORKING. I THEN SAID; 'I NEED TO KNOW OUR POS TO DETERMINE WHICH INST IS CORRECT TO KEEP FROM GETTING TOO FAR OFF COURSE DURING THE DEP PHASE.' HE WENT BACK ON THE RADIO JUST AS THE 1000 FT ALT WARNING WENT OFF; SO HE DIDN'T HEAR OR SEE IT. I WAS DISTR ALSO FOR THE SAME REASONS. THE SO CALLED OUT ALT. WE WERE AT 16500 FT WHEN I PUSHED THE ACFT OVER AND BACK TO 16000 FT -- OUR ASSIGNED ALT. THE CAUSE OF THIS WAS THE SAME AS SO MANY OTHERS. WE ALLOWED OURSELVES TO BE DISTR BY A PROB AND WERE NOT FLYING THE ACFT. I'VE BEEN INVOLVED IN NUMEROUS ABNORMAL AND EMER SITS AND NEVER ALLOWED THIS TO HAPPEN BEFORE; BUT ALL IT TAKES IS ONE TIME. ANOTHER LESSON LEARNED!