ACR FLC FAILS TO CATCH DROPPED WAYPOINT FROM FMS. A VERY MINOR TRACK DEV RESULTS.

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ORIGINAL CLRNC IN SFO ISSUED AS FILED TO LAX THEN T1J THEN DIRECT MEX. WE QUESTIONED THIS AS UNUSUAL; CTLR VERIFIED. CAPT PROGRAMMED 'DISCONTINUITY' AFTER LAX TO ENSURE WE VERIFIED CLRNC BEFORE LAX. PRIOR TO LAX WE WERE RECLRED AFTER LAX AS FILED LAX JLI J93 PPE HWD UJ5. WE WERE THEN CLRED DIRECT JLI; WHILE THE CAPT (PNF) REPROGRAMMED FOR REROUTE. I SELECTED DIRECT JLI FROM EXISTING FLT PLAN INFO AND VERIFIED. SOME TIME AFTER; ATC ASKED TO VERIFY WE WERE DIRECT JLI. WE LOOKED TO SEE WE WERE DIRECT DOWNLINE NAVAID. I BELIEVE IT WAS PTJ. WE INFORMED ATC WE WERE NOT DIRECT JLI. ATC RECLRED US DIRECT JLI. THE CORRECTION WAS SMALL AS I BELIEVE WE WERE ABOUT 1 MI OFF THE LAX-JLI TRACK. WHAT WAS MOST DISTURBING WAS NOT BEING SURE HOW IT HAD HAPPENED. WE BELIEVE IT HAPPENED BY CLRING A DISCONTINUITY NEAR 'BOTTOM' OF FLT PLAN BEFORE CLRING DISCONTINUITY AT TOP OF FLT PLAN WHICH IN THIS ACFT CAN CAUSE ALL OF FLT PLAN ABOVE SECOND DISCONTINUITY TO BE ERASED. IT IS ALSO POSSIBLE THAT MCDU WAS CALCULATING AS I ENTERED THE DIRECT INPUT. IN SOME CASES THIS ACFT WILL 'JUMP' TO ANOTHER POINT IN FLT PLAN AS YOU ENTER INFO; CAUSING INCORRECT INPUT. I WAS NEW IN ACFT AND STILL NOT COMPLETELY 'CONVERTED' FROM ANOTHER ACR INFO. BEING ON SMALLER SCALE ON NAV DISPLAY AND VERIFYING TO POINT ON NAV DISPLAY WOULD HAVE PREVENTED THIS. IN AN ATTEMPT TO COMPLY QUICKLY TO CLRNC; BOTH OF US ENTERED INFO IN COMPUTER AT THE SAME TIME; TAKING AWAY SOME ABILITY TO BACK EACH OTHER UP.