LCL CTLR CLRED A B727 INTO POS AND HOLD DURING IMC CONDITIONS WITH A COMMUTER ACFT ON FINAL APCH FOR THE SAME RWY. AFTER THE B727 HAD ALREADY CROSSED THE RWY HOLD LINE ABOUT 20 FT; THE CTLR INSTRUCTED THE ACFT TO HOLD. THE B727 FLC THEN OBSERVED THE LNDG ACFT APPEAR OUT OF THE RAIN AND LAND OVER THEM.

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TAXIING FOR TKOF AT ROC. CURRENT WX: FEW 700 FT; OVCST 7000 FT; 1 3/4 MI VISIBILITY; RAIN/MIST. RWY 22 IN USE. ILS GS OTS. SAME CTLR WORKING GND AND TWR FREQS! WE BEGAN OUR TAXI ON GND FREQ. APCHING THE HOLD SHORT LINE FOR RWY 22; WE SWITCHED TO TWR FREQ AND ADVISED WE WERE READY FOR DEP. CTLR CLRED US 'INTO POS AND HOLD RWY 22.' I ACKNOWLEDGED 'POS AND HOLD RWY 22.' BOTH CAPT AND I VISUALLY CLRED FINAL. CAPT CALLED FOR BEFORE TKOF CHKLIST 'BELOW THE LINE' AND BEGAN TO TAXI INTO POS AND HOLD. AS WE WERE ACCOMPLISHING THE CHKLIST; I OVERHEARD ANOTHER ACFT TALKING TO TWR; QUICKLY FOLLOWED BY TWR TELLING US TO HOLD SHORT OF RWY 22. AS TWR WAS TELLING US NOW TO HOLD SHORT; I LOOKED OUT TOWARD FINAL AND WAS SURPRISED TO SEE A COMMUTER ACFT APPEAR OUT OF THE RAIN ON SHORT FINAL FOR RWY 22. AT THE SAME TIME; I WAS TELLING TWR WE WERE ALREADY BEYOND THE HOLD LINE (BY ABOUT 20 FT). CAPT WAS APPLYING MAX BRAKES; BUT BECAUSE OF OUR ORIENTATION TO FINAL AND THE POS OF THE ACFT ON FINAL; HE WAS STILL UNAWARE OF THE REASON. AT THIS MOMENT; THE COMMUTER ACFT CREW NOTIFIED THE TWR THAT WE WERE NOT A FACTOR AND CONTINUED TO LAND. IT APPEARS THE ROC CTLR FORGOT ABOUT THE COMMUTER ACFT ON FINAL WHEN CLRING US INTO POS AND HOLD. WHEN CTLR CHANGED INSTRUCTIONS FOR US TO HOLD SHORT OF THE RWY; WE DID THE BEST WE COULD TO STOP. THE COMMUTER CREW WAS ALSO HEADS UP AND LUCKILY WE WERE ABLE TO STOP IN TIME TO PREVENT AN INCIDENT/ACCIDENT OR TO CAUSE THE COMMUTER TO ABORT ITS LNDG.