B757-200 CREW HAD A RWY INCURSION AT BFI.

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ISSUED A SOMEWHAT LENGTHY TAXI CLRNC FROM RAMP TO TAXI TO RWY 31L. CTLR SAYS WE WERE TOLD TO HOLD SHORT OF RWY 31R. I UNDERSTOOD CLRNC TO CROSS RWY 31R AND HOLD SHORT OF RWY 31L. WHEN I LOOKED DOWN FINAL TO CLR RWYS 31R AND 31L I SAW A JET ON FINAL FOR RWY 31L AND NO TFC LINED UP FOR RWY 31R. THIS FURTHER CONFIRMED MY BELIEF TO CROSS RWY 31R AND HOLD SHORT OF RWY 31L. I TAXIED ON RWY 31R AT TXWY A-4 AND THE GND CTLR TOLD US TO STOP. A SMALL SINGLE ENGINE CESSNA WAS ON A LONG FINAL FOR RWY 31L. THAT'S RIGHT; A SMALL PLANE WAS ON APCH TO THE S PARALLEL RWY WHEN THE AIRPORT WAS LNDG AND TKOF TO THE N. TO CORRECT SIT: SHORT AND CLR TAXI INSTRUCTIONS. KEEP TFC FLOW STANDARD WITH PARALLEL RWYS. ALL TKOF AND LAND THE SAME DIRECTION. SUPPLEMENTAL INFO FROM ACN 547995: WE HAD JUST PUSHED BACK ON THE CARGO RAMP AT BFI. I REQUESTED TAXI INSTRUCTIONS AND WAS CLRED TO 'RWY 31L VIA TXWY A4 AND B TO HOLD SHORT OF RWY 31R.' I WAS UNFAMILIAR WITH THE ARPT AND LOOKED DOWN AT MY ARPT DIAGRAM. WHEN I LOOKED UP; WE HAD JUST ENTERED RWY 31R (EXTREMELY SHORT TAXI; THIS EVENT TOOK PLACE IN SECONDS). CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: ON CALLBACK WITH THE FO RPTR SAID THE ACFT WAS AT TXWY A4 FROM THE PUSHBACK. WHEN SHE CALLED FOR TAXI CLRNC THE GND CTLR GAVE THE LONG TAXI CLRNC WITH THE 'HOLD SHORT OF RWY 31R' AT THE VERY END OF THE LONG CLRNC. SHE READBACK THE HOLD SHORT BUT FOR THE CAPT IT APPARENTLY DIDN'T SINK IN. SINCE THEY WERE ONLY A FOOT OR TWO FROM THE HOLD LINES; AS SOON AS THE BRAKES WERE RELEASED THEY WERE OVER THE LINE. RPTR THINKS THE HOLD SHORT SHOULD COME AT THE BEGINNING OF THE CLRNC; AND QUESTIONS THE TWR CTLR ALLOWING NOSE TO NOSE OP. THE CONFLICTING CESSNA WAS A C-152. THE CTLR HAD HIM DO A 360 AND HE THEN LANDED ON RWY 13R; MIDFIELD. THE TWR DID NOT REQUEST A TELEPHONE CALL FROM THE CREW.