ACFT CLEARED INTO ADJACENT AIRSPACE ON A ROUTE THAT WAS CONTRARY TO PREFERRED ROUTE REQUIRED IN LETTER OF AGREEMENT.

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SMT X ON IFR FLT PLAN CLRD TO MDSD VIA; 'RADAR VECTORS G-3 MELLA G-3 MDSD.' ACFT DEPARTED AND THE DEP CTLR ISSUED; 'PROCEED DIR BQN ON COURSE.' BQN WAS NOT ON THE ACFT ROUTE OF FLT. I; AS THE CENTER CTLR; TOOK THE HANDOFF BUT DUE TO OUR FDRS PROB I DID NOT HAVE THE FLT STRIP AND BY THE COORD WITH THE DEP CTLR I KNEW THAT THE ACFT WAS GOING BQN ON COURSE. I ASSIGNED THE ACFT FL220 AND WENT TO TAKE CARE OF OTHER ACFT THAT NEEDED MY ATTN. THE ACFT WAS W OF BQN GOING TOWARD MELLA LEVEL AT FL220. I LOOKED AT THE BAY; AND HIS STRIP WAS THERE COORDINATED AT FL220. I TERMINATED RADAR SVC WITH THE ACFT; SWITCHED ACFT TO MDSD ABOUT 20 MI INSIDE SJU AIRSPACE. A FEW MINS LATER MDSD CALLED SAYING THAT THE ACFT HAD NOT SHOWN UP AT MELLA BUT 15 MI TO THE N. THESE I BELIEVE WERE CONTRIBUTING FACTORS: THE ACFT ORIGINALLY FILED SJU B520 BQN B520 MDSD. CLRNC DELIVERY CHANGED HIS ROUTE TO G-3 MELLA G-3 MDSD. DEP CTLR GAVE ACFT; 'DIR BQN ON COURSE.' BQN WAS NOT ON HIS CLRNC. I; AS CENTER CTLR DID NOT HAVE A FLT STRIP ON ACFT BECAUSE OUR FDRS SYS HAS NOT BEEN PRINTING STRIPS CORRECTLY FOR THE LAST 3 WKS. THIS MEANS THE D CTLR HAS TO REQUEST EVERY STRIP HE NEEDS MANUALLY AND HAS TO WAIT FOR THAT STRIP TO BE FINISHED PRINTING BEFORE HE CAN REQUEST ANOTHER. THE PLT ASSUMED THAT AFTER BQN HE WAS TO GO DIR MDSD EVEN THOUGH HIS CLRNC DID NOT HAVE BQN ON IT.