AN MD83 FLT CREW EXPERIENCE AN ANOMALY IN THE FMS SYS.

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ENRTE FROM XXX TO STL; WE WERE RECLRED DIRECT DXV (POCKET CITY) THEN THE QBALL ARR TO STL. WORKLOAD WAS MODERATE DUE TO TSTM DEVS. WE HAD PLANNED ON A RWY 30L ARR. ENRTE; THE STL ATIS INDICATED RWY 12R AT STL. I WENT TO THE ARR AND DEP PAGE AND CHANGED THE SELECTED RWY TO RWY 12R. I HAD THE FO VERIFY THE CHANGE. WE THEN NOTICED THE QBALL ARR HAD DROPPED OUT. SO THEN I RE-ENTERED THE CORRECT FLAVOR OF QBALL ARR. (WE HAVE ABOUT 6 DIFFERENT QBALLS DEPENDING ON RWY OR APCH IN USE.) I CLOSED THE ENRTE DISCONTINUITY AND ENTERED THE APPROPRIATE XING RESTR FOR QBALL; IE; 15000 FT. THE FO VERIFIED THE CORRECT ARR AND ALSO MY EXECUTING THE XING RESTR ON THE LEGS PAGE. WHAT BOTH MY FO AND MYSELF FAILED TO NOTICE WAS THAT THE MARION TRANSITION DROPPED OUT. ROUTING IS HARD TO SEE AS YOU APCH THE 320 NM RANGE. AFTER POCKET CITY; THE ACFT WAS FLYING DIRECT TO QBALL RATHER THAN TOWARDS MARION VOR. THE CTLR THEN ASKED IF WE WERE ON A HDG AND I SAID NO. HE THEN CLRED US DIRECT TO QBALL. JUST BECAUSE AN ARR GATE IS ENTERED AND BEING FLOWN TO AND THE PROPER ARR ENTERED; DOESN'T MEAN THE TRANSITION BTWN THAT FIX AND ARR IS ENTERED. I WILL WATCH FOR THIS TRAP.