ERROR IN FMS SOFTWARE DROPPED OUT WAYPOINTS AND; WITH ACFT ON AUTOPLT; ACFT MADE PREMATURE TURN. APCH CTLR INTERVENED AND TURNED FLC ACFT IMMEDIATELY. AT THE SAME TIME RPTR FLC RECEIVED A TCASII ALERT AND RPTS AN NMAC.

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WE WERE USING THE SPZ8000 WITH THE NZ2000; 4.0 SOFTWARE. I WAS LOOKING OUTSIDE; THE FO WAS CHANGING FREQ WHEN THE ACFT TURNED TO A 300 DEG HDG; WHICH WAS NOT SUPPOSED TO HAPPEN UNTIL PASSING THE NEXT INTXN. I ASKED THE FO IF WE HAD PASSED THAT POINT AND HE DIDN'T KNOW. APCH CTL TOLD US TO MAKE AN IMMEDIATE L TURN; AT THE SAME TIME WE GOT AN RA ON THE TCASII. WE CALLED HONEYWELL AFTER WE GOT ON THE GND AND FOUND OUT THAT THE SOFTWARE WAS A GLITCH IN THE PROGRAM THAT ALLOWS THE ACFT TO MAKE AN INCORRECT HDG CHANGE PRIOR TO YOUR SELECTED HDG CHANGE. THE FLT PLAN READ FROM-TO; WHEN IT SWITCHED TO-TO PRIOR TO THE SELECTED POINT WE SHOULD HAVE BEEN AWARE OF THIS PROB BUT HONEYWELL ENGINEER HASN'T INFORMED ALL USERS OF IT. WE SHOULD HAVE BEEN MORE AWARE OF OUR POS; BUT WEREN'T. THIS SYS IS IN MANY CORP AND ACR ACFT. WE TRAIN; AND NOWHERE DURING THIS TRAINING DID ANYBODY MENTION THIS PROB. WE ARE CURRENTLY CHANGING TO THE 4.1 SOFTWARE SO AS NOT TO HAVE THIS PROGRAM PROB AGAIN. SUPPLEMENTAL INFO FROM ACN 334242: WHILE I WAS CHANGING NAV #1 AND NAV #2 BACK TO 11L; WE CROSSED WOLUS INTXN. NEXT WE RECEIVED AN EICAS MESSAGE; 'COUPLED DATA INVALID.' I QUESTIONED THE PF WHAT HE DID TO RECEIVE THIS MESSAGE. HE STATED HE DID NOT TOUCH ANYTHING. WE CHKED THE FMS'S; AND ALL OTHER DATA AND COULD NOT FIND ANY DISCREPANCIES. I SUSPECT THAT THE PF DID INDEED EITHER PUSH A NAV #1 SELECTOR BUTTON WHILE HAVING LNAV SELECTED. THIS PLT IS NOT WHAT ONE WOULD CONSIDER AN EXPERT FMS OPERATOR. VERY SHORTLY AFTER WE LANDED I CALLED HONEYWELL; THE MANUFACTURER OF THE FMS; TO DETERMINE WHY AND HOW THIS HAPPENED. HE SAID THERE IS A WELL KNOWN GLITCH IN OUR CURRENT VERSION OF THE SOFTWARE (4.0) THAT WOULD CAUSE THE FMS TO SKIP 2 WAYPOINTS; AS THOUGH YOU HAVE PASSED THEM.