ACR X HAD LTSS FROM ACR Y XING RWY. ACR X ABORTED TKOF. SYS ERROR.

Narrative

I WAS WORKING ARRS INTO JFK. ANOTHER CTLR WAS WORKING DEPS. ALL ARRS MUST CROSS DEP RWY TO TAXI TO THEIR GATES. DEP CTLR GIVES XING CLRNC TO ARR CTLR. DEP CTLR TURNED TO ME AND ADVISED HE WAS HOLDING ACFT IN POS SO I COULD CROSS THE RWY. I ASKED IF HE WOULD RATHER WAIT A FEW ACFT BECAUSE I SAW HIS SECOND AND THIRD ACFT GOING OVER SOME FIX WHICH HAD IN TRAIL RESTRICTIONS. HE SAID NO BECAUSE HIS LAST DEP WAS THE SAME FIX AS THE ONE IN POS AND HAD TO WAIT FOR THAT IN TRAIL RESTRICTION SO I COULD CROSS. I INSTRUCTED 3 ACFT TO CROSS AND WALKED OVER TO THE ASDE TO OBSERVE THEM. I SCANNED THE RWY AND DID NOT OBSERVE ANY OTHER ACFT THAT I CONSIDERED A PROBLEM. AS THE ACFT WERE XING; THE DEP CTLR TURNED TO ME AND EXCLAIMED 'ARE YOU XING?' 2 ACFT WERE CLR AND I WAS UNABLE TO HOLD THE THIRD SHORT. THE DEP HAD CLRED AN ACR X FOR TKOF PRIOR TO THE ONE HE WAS HOLDING FOR MY XING. ACR X ABORTED TKOF AFTER SEEING THE FIRST ACR Y XING THE RWY APPROX 2000 FT FROM ROLLING POINT. THE DEP CTLR DID NOT LEAVE THE DEP FLT PROGRESS STRIP IN THE STRIP BAY AS PER JFK ORDER ON STRIP MGMNT; BUT PLACED IT ON THE COUNTER IN FRONT OF HIM WHERE I COULD NOT SEE IT. THAT SPACE; IAW ORDER; IS LEFT FOR ARRS; AS I HAD MINE; SO HE COULD SEE MY TFC AND ISSUE XING CLRNC. HAD THE STRIP BEEN IN THE BAY; I WOULD HAVE FURTHER QUESTIONED THE XING CLRNC. A SIMILAR SITUATION HAPPENED SEVERAL YRS AGO WHICH PROMPTED THE ORDER ON STRIP MGMNT TO ENSURE THAT EVERYONE COULD EASILY SEE AND UNDERSTAND EVERYONE ELSE'S TFC.