CGA JET TAXIING OUT FOR TKOF FAILS TO HOLD SHORT OF RWY WHILE AN ACR IS LNDG.

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CGA X REQUESTED TO TAXI FROM FBO. I ISSUED 'RWY 22L. TAXI VIA 'W;' 'N' HOLD SHORT OF RWY 31C.' THE PLT DIDN'T READBACK ANY OF THE CLRNC; BUT DID START TO TAXI. I MONITORED THE PROGRESS OF CGA X AS IT TAXIED VIA THE RTE ISSUED. RWY 31C WAS ACTIVE WITH LNDG AND DEPARTING ACR ACFT. AS CGA X APCHED THE DEP END OF RWY 31C; I AGAIN ISSUED INSTRUCTIONS TO 'HOLD SHORT OF RWY 31C;' TO WHICH CGA X AGAIN DID NOT ACKNOWLEDGE. I ONCE AGAIN ISSUED THE INSTRUCTIONS FOR CGA X TO HOLD SHORT OF RWY 31C. THIS TIME THE PLT REPLIED 'CGA X HOLDING.' BY THIS TIME; CGA X WAS ALREADY ON RWY 31C AS ACR Y; AN MLG; WAS IN THE LNDG ROLLOUT. CGA X STOPPED IN THE INTXN OF RWY 31C AND 22R. SUPPLEMENTAL INFO FROM ACN 236325: WE WERE GIVEN A RWY CHANGE TO RWY 22L VIA W AND N. I ACKNOWLEDGED THE NEW INSTRUCTIONS; BUT DID NOT HEAR; NOR DID OTHER CREW MEMBER; HOLD SHORT INSTRUCTIONS FOR RWY 31C. SUBSEQUENT CONVERSATION WITH THE TWR SUPVR REVEALED THAT THE TAPES SHOWED THESE INSTRUCTIONS WERE GIVEN! IF THEY WERE GIVEN; NEITHER OF US IN THE COCKPIT HEARD IT AND NEITHER OF US REMEMBER THE GND CTLR ASKING US TO CONFIRM THE HOLD SHORT INSTRUCTIONS. MENTALLY; WE WERE READY TO TAXI ALL THE WAY TO 22L.