A GIV CREW DISTR BY A HYD SYS ANOMALY AFTER LNDG AT BOS FAILED TO HOLD SHORT OF AN ACTIVE RWY FORCING LNDG TFC TO GO AROUND.

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AFTER LNDG ON BOS RWY 4R; TWR CLRED US TO EXIT L-HAND ONTO DIAGONAL RWY 33R; SWITCH TO RWY 4L TWR FREQ AND MONITOR; HOLD SHORT OF RWY 4L AND FOLLOW ACFT IN FRONT. AFTER EXITING WE SWITCHED FREQ AND BEGAN TAXIING TOWARD ACFT IN FRONT MONITORING XING INSTRUCTIONS BEING GIVEN BY 4L TWR TO ACFT IN FRONT. WHEN THE COPLT BEGAN RETRACTING THE FLAPS AND GND SPOILERS; THE AUX HYD PUMP LATCHED ON WHICH IS NOT NORMAL. THIS CAUSED OUR ATTN TO BE DIVERTED FOR A MOMENT. I CONTINUED FOLLOWING THE ACFT AHEAD WHEN 4L TWR CTLR CALLED OUR TAIL NUMBER. I IMMEDIATELY BROUGHT THE ACFT TO A STOP RECOGNIZING I HAD FOLLOWED THE ACFT IN FRONT PAST THE HOLD SHORT LINE BUT STILL SHORT OF THE ACTIVE RWY WITHOUT POSITIVE CTLR CONFIRMATION. AN ACFT (REGIONAL TYPE) WAS ON FINAL FOR 4L AT AN APPROX ALT OF 200 FT AGL. TWR CTLR AFTER CONTACTING US AND OUR STOPPING CALLED THE ACFT ON APCH AND ADVISED THEM TO GO AROUND EVEN THOUGH WE WERE SHORT OF THE ACTIVE. TWR THEN CLRED US TO CROSS 4L TURN L-HAND ON TXWY N AND CONTACT GND CTL WHO GAVE US TAXI INSTRUCTION TO THE RAMP. SUPPLEMENTAL INFO FROM ACN 698053: AS WE WERE ROLLING TOWARD THE MD80; I WAS RUNNING THE AFTER LNDG CHKLIST. WE WERE MOMENTARILY DISTR DURING THIS TIME BY AN AUX HYD PUMP THAT ACTIVATED WHEN THE ACFT BRAKES WERE APPLIED. THE PUMP RESET AND REMAINED OFF WHEN RE-ARMED (IT SHOULD BE OFF DURING TAXI WITH THE MAIN HYD SYS OPERATING). BEFORE WE REACHED THE MD80; IT WAS CLRED TO CROSS RWY 4L (I DID NOT HEAR THE CLRNC; BUT HE BEGAN TO CROSS BEFORE WE CAUGHT UP). WE INADVERTENTLY FOLLOWED AND OUR NOSEWHEEL CROSSED THE HOLD SHORT LINE BEFORE TWR CALLED AND TOLD US TO HOLD OUR POS.