DC9 ACFT AFTER LNDG WITH TAXI INSTRUCTIONS. DUE TO FREQ CONGESTION FLC WAS UNABLE TO CONFIRM CLRNC TO THE GATE; BUT PROCEEDED ASSUMING THAT. JUST AS THEY STARTED TO CROSS AN ACTIVE RWY AN ACFT TOOK OFF JUST OVER AND IN FRONT OF THEM WITHIN 50 FT. WHEN QUESTIONING TWR THEY WERE TOLD THAT THE CLRNC WAS TO HOLD SHORT OF THE RWY.

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AFTER LNDG ON RWY 12R AT HOU; WE EXIT THE RWY BY TXWY L. TWR CTLR INSTRUCTED US TO MAKE L TURN ON TXWY M AND HOLD SHORT OF RWY 22; AND INFORMED US; HIM WORKING GND ON TWR FREQ (AT THE TIME HE WAS WORKING RWYS 12R; 12L; AND 22). AFTER DEP OF AN AIRPLANE; WE WERE GIVEN A CLRNC TO CROSS RWY 22 VIA TXWY M; TXWY H TO THE GATE. DUE TO THE CONGESTION OF FREQ; FO COULD NOT READ BACK THE SECOND SET OF INSTRUCTIONS AND ANSWERED WITH A ROGER AND STARTED RUNNING HIS AFTER LNDG FLOWS. WE CROSSED RWY 22 ON TXWY M AND RIGHT AFTER MAKING A R TURN ON TXWY H; I LOOKED L TO CLR RWY 12L. WHAT I SAW WAS A TWIN ENG COMMUTER TAKING OFF IN DARK. ALL HE HAD ON WAS HIS POS LIGHTS AND ROTATING BEACON ON AT OUR 10 O'CLOCK POS; AIRBORNE 4-5 FT AGL. I MADE PANIC STOP THE AIRPLANE; BY THIS TIME 2-3 FT BEYOND THE HOLD SHORT LINE. WE WERE STILL CLR OF THE RWY AFTER DEPARTING AIRPLANE CLRED. WE CALLED THE TWR/GND AND ASKED HIM WHY WE WERE CLRED TO THE GATE. HE INFORMED US THAT OUR CLRNC WAS TO HOLD SHORT OF RWY 12L. AFTER GETTING ANOTHER CLRNC TO CROSS THE RWY WE TAXIED TO THE GATE. LATER I TALKED TO THE TWR SUPVR; AND HE INFORMED ME THAT HE LISTENED TO THE TAPES AND ASSURED ME THAT THE CTLR WAS RIGHT AND ISSUED HOLD SHORT INSTRUCTIONS. IF HE DID; THEN IT HAD TO BE BLOCKED BY ANOTHER AIRPLANE; BECAUSE WE NEVER HEARD HOLD SHORT INSTRUCTION. IT WOULD BE GREAT HELP IF DEPARTING COMMUTER HAD HIS LNDG LIGHTS ON AND BE SEEN BY OTHERS. IT WOULD BE GREAT IF CTLRS WOULD NOT TAKE TOO MUCH WORK ON THEMSELVES. IT WOULD BE VERY SMART IF WE WOULD QUESTION OUR CLRNC AT LEAST TWICE; OR MORE.