PLT OF A320 ENCOUNTERS DIFFICULTIES PROGRAMMING WAYPOINTS INTO THE THALIS FMGS.

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CRUISING AT FL350 AND NAVING DIRECT TO PIE VOR; I MADE A WAYPOINT APPROX 35 MI NW OF PIE VOR FOR A XING RESTR I HEARD ISSUED TO OTHER ACFT IN FRONT OF US; IN ANTICIPATION OF ISSUANCE OF SAME CLRNC FOR US AND EXPLAINED TO MY WHAT THAT WAYPOINT WAS. A FEW MINS LATER; AND CHKING IN WITH ANOTHER JAX CTLR; HE ISSUED US A NEW WAYPOINT APPROX 90 MI NW OF PIE VOR TO CROSS AND MAINTAIN FL250. IN THE SPIRIT OF KEEPING ALL NAV ON 'MANAGED MODE' I PROCEEDED WITH CREATING A WAYPOINT IN FMGS FOR OUR NEW XING RESTR. AFTER THAT; I PROCEEDED TO CLOSE THE DISCONTINUITY AND THAT'S WHEN I STARTED TO HAVE PROBS WITH FMGS. FIRST; IT WOULD NOT CLOSE THE DISCONTINUITY AND WOULD NOT ALLOW ME TO DELETE THE PREVIOUSLY CREATED WAYPOINT AT PIE 35 DME AND EVEN CREATED AN IMAGINARY HOLDING PATTERN FOR THE 90 DME WAYPOINT OUT OF NOWHERE WITHOUT ANY PLT INPUT. AS THE LAST RESORT; WHILE FO WAS TRYING TO HELP AND TROUBLESHOOT THE STRANGE BEHAVIOR OF THE FMGS; I CHOSE TO STOP ALL THIS AND GO DIRECT TO PIE TO DUMP ALL THESE WAYPOINTS AND START ALL OVER AGAIN; BUT TO NO AVAIL -- FMGS WOULD NOT ALLOW ('NOT ALLOWED') A SIMPLE DIRECT TO A DOWN LINE WAYPOINT. THIS WAS MY FIRST TIME TO SEE A BREAKDOWN AND REFUSAL OF SIMPLE TASKS BY A THALIS FMGS. AT THIS POINT WE WERE GONE TOO FAR AND IT WAS TIME TO START THE DSCNT TO FL250. I ASKED THE FO TO FIND OUT HOW FAR WE WERE FROM PIE VOR -- AND TO MY HORROR; WE WERE JUST ABOUT 95 MI AND STILL AT FL350. I INCREASED THE RATE OF THE DSCNT; BUT MEETING OUR XING RESTR WAS HOPELESSLY BEYOND MY REACH. WE CROSSED THE POINT AT ABOUT +6000 FT. TALKING TO THE CTLR ABOUT MY LATE DSCNT AND NOT BEING ABLE TO MEET THAT RESTR; HE CALMLY REPLIED; 'I SEE THAT YOU ARE NOT GOING TO MAKE THE XING. DO THE BEST YOU CAN.' WE LEVELED AT FL250 TO THE BEST OF MY KNOWLEDGE AT PIE 84 DME; AND SECONDS LATER; WE WERE HANDED OFF TO ANOTHER CTLR WITHOUT ANY FURTHER COMMENT BY THE CTLR. I HAVE LEARNED A VALUABLE LESSON! TO THE BEST OF MY KNOWLEDGE; THERE WERE NO LOSS OF SEPARATIONS INDICATED EITHER BY MY ONBOARD TCASII EQUIP OR BY THE ATC CTLR.