MISCOM FLC GND CTLR. GND CTLR INITIALLY CLRED FLC TO HOLD SHORT OF TXWY S ENRTE TO THE TKOF RWY; BUT THEN CALLED THEM AGAIN AND CLRED THEM TO THE RWY WHICH CANCELED THE PRECEDING HOLD SHORT CLRNC. AS RPTR TAXIED ACROSS A RWY EXTENSION; AN ACFT HAD MADE THE TKOF OVER THE TOP OF THEM.

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I WAS CAPT ON FLT TO PHL. WE CALLED FOR TAXI AND GIVEN THE FOLLOWING INSTRUCTIONS: 'TAXI TO RWY 36C VIA TXWY A AND TXWY C; HOLD SHORT OF TXWY S.' WE READ BACK THE CLRNC INCLUDING THE HOLD SHORT. ABOUT 1 MIN LATER; WE WERE CALLED BY GND WHO SAID 'TAXI TO RWY 36C.' WE ACKNOWLEDGED THE CLRNC AND CONTINUED TAXIING PAST TXWY S TOWARD RWY 36C. AS WE PASSED TXWY S; I NOTICED LIGHTS COME ON AN ACFT ON RWY 36C WHICH I TOOK TO BE AN ACFT IN TKOF POS. A FEW SECONDS LATER I REALIZED IT WAS MOVING AND ON ITS TKOF RUN. I CONTINUED TAXIING BECAUSE MY POS PUT ME RIGHT IN LINE WITH RWY 36C EXTENSION AND THE ACFT PASSED OVER OURS AT ABOUT 150 FT. GND ABOUT THIS TIME CALLED US AND SAID WE WERE SUPPOSED TO HOLD AT TXWY S; BUT WE CORRECTED HIM AND REMINDED HIM WE WERE CLRED TO TAXI RWY 36C; CANCELING OUR HOLD INSTRUCTIONS. THERE WAS NO FURTHER DISCUSSION ON THE RADIO ABOUT THE INCIDENT. IT IS HARD TO THINK OF WHAT WE COULD HAVE DONE DIFFERENTLY. WHEN I FIRST SAW THE ACFT I BELIEVED IT WAS MERELY IN POS WITH LIGHTS ON. INDEED; AS WE APCHED THE END OF TXWY C AND SWITCHED TO TWR; I HEARD TWR CLR AN ACFT IN POS AND HOLD WHILE TFC PASSED DOWNFIELD; SO THIS WAS A COMMON SIT. I BELIEVE GND EITHER FORGOT ITS CLRNC TO US; MISTOOK US FOR ANOTHER ACFT WHEN THEY CLRED US TO 'TAXI RWY 36C;' OR DIDN'T COORDINATE WITH TWR. ONCE I REALIZED THE ACFT WAS TAKING OFF; I COULDN'T STOP AS WE WERE IN LINE WITH THE RWY EXTENSION.