ACFT X TKOF ON OCCUPIED RWY HAD LTSS FROM VEHICLE Y. SYS ERROR.

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I WAS WORKING LCL AND GND COMBINED AT SYRACUSE HANCOCK INTL ARPT. MAIN RWY (10/28) WAS CLOSED FOR CONSTRUCTION AND PAINTING. VEHICLE Y REQUESTED TO CROSS RWY 32 AT 'A' TXWY. I TOLD HIM TO HOLD SHORT. I DIDN'T RECEIVE HIS ACKNOWLEDGE HOLDING SHORT--WHICH HE DID. I CLRED 2 MORE ACFT FOR TKOF AND THEN PUT ACFT X INTO POS AND HOLD. I THEN TOLD Y TO CROSS RWY 32 AT TXWY 'A' AND PROCEED TO RWY 10. WHEN I OBSERVED A VEHICLE CLRING THE RWY I CLRED X FOR TKOF. A FEW SECONDS LATER X ASKED IF I KNEW THERE WAS A VEHICLE ON THE RWY. I TOLD HIM TO HOLD HIS POS. I QUERIED Y ON WHY HE DIDN'T TELL ME HE HAD A SECOND VEHICLE 'WITH HIM.' HE RESPONDED THAT HE AND COMPANY WERE CLR OF THE RWY. I CLRED X FOR TKOF. SUPPLEMENTAL INFO FROM ACN 279917: Y CALLED THE GND CTLR TO CROSS RWY 32 ON TXWY ALPHA. Y DID NOT SAY THAT HE HAD ANOTHER VEHICLE WITH HIM. Y WAS CLRED TO CROSS THE RWY AND PROCEEDED TO DRIVE ACROSS RWY 32 WBOUND WITH THE SECOND VEHICLE FOLLOWING. WHILE THE SECOND VEHICLE WAS ON THE RWY; ACFT X SPOTTING THE TRUCK. THE PLT CALLED THE TWR STATING THAT THERE WAS A VEHICLE ON THE RWY AND THE ACFT SLOWED BUT DID NOT STOP. THE TWR ASKED IF THE ACFT COULD TAKE IT FROM IT'S PRESENT LOCATION AND IT PROCEEDED TO DEPART.