FATIGUED FLT CREW OF MD88 IS SLOW TO ARREST DSCNT ACCELERATED BY MALFUNCTIONING AUTOPLT. OVERSHOOT CLRED ALT BY 500 FT.

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THIS EVENT OCCURRED ON OUR 5TH LEG OF THE DAY AFTER APPROX 13 HRS ON DUTY. ABOUT 15 MINS PRIOR TO EVENT; WE NOTICED THAT THE #1 AUTOPLT BEGAN A MILD PORPOISE OF +/-40 FT AT CRUISE ALT WITH ASSOCIATED AUTOTHROTTLE CYCLING TO MAINTAIN SPD. WE ATTEMPTED TO TROUBLESHOOT THE PROB BY ALTERNATING BTWN 'VNAV' AND 'ALT HOLD' MODES; AUTOTHROTTLES ON AND OFF; AND SELECTING #2 AUTOPLT. THE PORPOISING ISSUE CONTINUED AND WE SENT A MESSAGE VIA ACARS TO MAINT CTL TO INFORM THEM OF THE PROB. WE CONTINUED THE FLT WITH #2 AUTOPLT ENGAGED. WE WERE GIVEN A DSCNT A FEW MINS LATER BY ZBW TO FL240 AND MAINTAIN 310 KTS. THE DSCNT WAS ACCOMPLISHED WITH #2 AUTOPLT IN VNAV MODE WITH 310 KTS SELECTED IN FMS OVERRIDE. APCHING FL245 WITH A DSCNT RATE OF 1000 FPM; THE AUTOTHROTTLES SUDDENLY WENT TO EPR CLB MODE (WITH ASSOCIATED AUTOTHROTTLE ADVANCE TO CLB PWR) AND THE NOSE PITCHED DOWN SHARPLY. THE DSCNT RATE INSTANTLY INCREASED TO 3000 FPM AND I ENGAGED 'VERT SPD MODE' TO ARREST THE DSCNT. THIS HAD NO EFFECT AND I PRESSED THE 'ALT HOLD' BUTTON; WHICH ALSO HAD NO EFFECT. I IMMEDIATELY DISENGAGED THE AUTOPLT AND AUTOTHROTTLES BUT WE WERE ALREADY PASSING THROUGH FL240. I WAS ABLE TO MANUALLY STOP THE DSCNT BY FL235 AND WAS CLBING BACK TO FL240 WHEN ATC CLRED US TO FL230. THE REST OF THE FLT WAS FLOWN MANUALLY AND WE LANDED IN BOSTON UNEVENTFULLY. ZBW MADE NO MENTION OF THE ALTDEV. WE WERE MET BY MAINT AT THE GATE WHERE WE RELATED THE ENTIRE INCIDENT AND RECORDED IT IN THE ACFT LOGBOOK. I FELT THAT WE HANDLED THE INCIDENT IN A SATISFACTORY MANNER BUT OUR REACTION TIME WAS DEFINITELY SLOWED DUE TO FATIGUE.