FLC OF A B757 LOST CTL TEMPORARILY DURING LNDG ROLL WHEN THE ACFT STARTED BOUNCING; CAUSING THE CAPT A DELAY IN TURNING OFF THE AUTOBRAKES TO USE THE NORMAL BRAKING. THE ACFT WAS CHKED BY COMPANY MAINT FOR DAMAGE PRIOR TO TAXIING TO GATE. THE R FLAP WAS DAMAGED. THE RWY CONDITION WAS BELIEVED TO HAVE CAUSED THE BOUNCING; WHETHER BY CONDITION OR FOREIGN OBJECTS.

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HELD UP FOR A FEW MINS DUE TO TSTM OVER ARPT IN SJU. ACFT AHEAD OF US MADE NORMAL APCH AND LNDG AND WE WERE CLRED FOR APCH. NORMAL APCH AND LNDG RWY 8. AUTOSPOILERS AND AUTOBRAKES 2 WERE SELECTED. SMOOTH LNDG AND ROLLOUT BY FO. AT ABOUT 100 KTS; I SAID I HAD THE AIRPLANE. TO MAKE A NORMAL TURNOFF; I REACHED FOR THE AUTOBRAKE SWITCH AND GOT READY TO START USING NORMAL BRAKING WHEN THE ACFT BEGAN A VIOLENT SERIES OF BOUNCES ON THE RWY. THE MOTION WAS SO VIOLENT THAT WE COULD BARELY SEE THE PANEL AND AT FIRST I COULD NOT GET TO THE AUTOBRAKE SWITCH OR APPLY THE BRAKES. AS WE DECELERATED THROUGH ABOUT 40-50 KTS; I WAS ABLE TO REGAIN CTL AND STOP THE ACFT AND CLR THE RWY. WE STOPPED THE ACFT JUST CLR OF THE RWY AND CALLED FOR THE CRASH CREW AND MAINT TO INSPECT THE ACFT. I ASKED THE PAX TO REMAIN CALM AND WE WOULD LET THEM KNOW WHAT HAD HAPPENED WHEN WE HAD A CHANCE TO ASSESS THE SIT. WE LEFT THE FLAPS EXTENDED; AS I THOUGHT THE PROB MAY HAVE BEEN A BLOWN TIRE AND DEBRIS MAY HAVE DAMAGED THE FLAPS. THE CRASH CREW ARRIVED FIRST AND ON GND CTL I ASKED THAT A VISUAL CHK OF THE ACFT BE MADE TO SEE IF IT LOOKED OK TO TAXI TO THE TERMINAL. SHORTLY THEREAFTER; COMPANY MAINT ARRIVED AND GAVE US HAND SIGNALS TO ROLL FORWARD SOME. THE FO THEN SPOKE WITH MAINT AND ASKED IF THE ACFT LOOKED OK TO TAXI AND TO RAISE THE FLAPS. HE WAS TOLD THAT EVERYTHING LOOKED OK AND OK TO RAISE THE FLAPS. WE TAXIED TO THE GATE WITHOUT INCIDENT. AFTER PARKING; DAMAGE WAS NOTED TO THE R FLAP.