A B727 FLC CLBS TO FL250 BEFORE THEY REALIZE THAT THE INBOARD FLAPS HAVE NOT RETRACTED FROM THEIR 15 DEG POS. DURING DSCNT THE CREW FAILS TO NOTE THE CAUTION NOTE ABOUT 'NOT LOWERING THE ABNORMAL FLAPS WITH THE ALTERNATE FLAP SWITCH.' THE ACFT HAD A DEFECTIVE INBOARD FLAP MOTOR.

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AFTER TKOF THE INBOARD FLAPS DID NOT RETRACT. THIS WAS NOT NOTICED BY THE FLC UNTIL FL250 AND 300 KIAS; WHICH EXCEEDED THE FLAP LIMIT SPD AND ALT. WE DSNDED AND REDUCED THE AIRSPD TO WITHIN FLAP LIMITS. WE THEN COMPLETED THE ABNORMAL FLAP CHKLIST; HOWEVER; WE LOWERED THE FLAPS TO 30 DEGS FOR LNDG WHICH VIOLATED A 'CAUTION' IN THE CHKLIST. MISSING THE CAUTION WAS UNINTENTIONAL. THE ACFT LANDED NORMALLY WITHOUT INCIDENT. TAKING OFF INTO THE SUNSET CONTRIBUTED TO US NOT NOTICING THE INBOARD FLAP NEEDLES NOT MOVING. WE COMPLETED THE ABNORMAL FLAP CHKLIST DOWN TO THE APCH AND WHEN WE RETURNED TO THE CHKLIST ON APCH MISSED THE 'CAUTION' REGARDING 'NOT MOVING THE ABNORMAL FLAPS WITH THE ALTERNATE FLAPS SWITCH BECAUSE OF A LACK OF ASYMMETRY PROTECTION.' THE FLAPS WERE LOWERED TO 30 DEGS AND A NORMAL LNDG FOLLOWED. WHEN BRIEFING THE ABNORMAL SIT; I SHOULD INCLUDE A REMINDER TO NOTE ALL 'WARNINGS AND CAUTIONS.' SUPPLEMENTAL INFO FROM ACN 393616: I REMEMBER CHKING 'FLAPS...UP' BY VERIFYING FLAP HANDLE POS; LEADING EDGE FLAPS OUT OF POS LIGHTS EXTINGUISHED; AND OUTBOARD TRAILING EDGE FLAP GAUGE AT ZERO DEGS. I DO NOT REMEMBER CHKING THE INBOARD FLAP POS GAUGE; WHICH IS LOCATED BELOW THE OUTBOARD ON THE FORWARD PANEL. CLBING THROUGH 10000 FT THE CAPT AND MYSELF NOTED THE 'WINDSHEAR FAIL' LIGHT ILLUMINATED. AFTER RESETTING THE CIRCUIT BREAKERS WE DECIDED THE SYS WAS INOP AND ENTERED IT IN THE MAINT LOGBOOK. WE DID NOT MAKE THE CONNECTION BTWN A FLAP POS PROB AND THE WINDSHEAR COMPUTER BECAUSE THERE WERE NOT ENOUGH CLUES AT THIS POINT SINCE WE THOUGHT ALL ELSE WAS NORMAL. AT ABOUT FL250; IN THE CLB; THE CAPT SAID 'THE INBOARD FLAPS ARE SHOWING FLAPS 15 DEGS.' THE LIMITS FOR FLAPS 15 DEGS ARE MAX ALT FL200 AND 205 KTS; SO WE SLOWED AND DSNDED. WE CONSULTED THE COMPANY 'TRAILING EDGE ABNORMAL CHKLIST' (WHICH SEEMED TO BE WRITTEN MORE FOR AN ASYMMETRICAL SIT THAN A SYMMETRICAL FAILURE LIKE WHAT WE HAD) AND DECIDED TO PROCEED TO OUR DEST AND ATTEMPT A NORMAL FLAP EXTENSION AND NORMALLNDG. WE ALSO DECIDED THAT WE WOULD DISCONTINUE THE ABNORMAL CHKLIST UNLESS IT BECAME NECESSARY TO COMPLETE IT ON FINAL. THE REST OF THE ARR WAS NORMAL UNTIL WE BEGAN CONFIGURING FOR LNDG. THE OUTBOARD AND LEADING EDGE FLAPS EXTENDED NORMALLY BUT THE INBOARD FLAPS REMAINED AT 15 DEGS; SO THE CAPT TOLD THE COPLT TO EXTEND THE FLAPS USING THE ALTERNATE FLAP SYS AND TOLD ME TO CONTINUE THE ABNORMAL CHKLIST. INSTEAD OF PICKING UP THE CHKLIST WHERE I HAD LEFT OFF; I PROCEEDED DIRECTLY TO THE ACTION IN THE CHKLIST THAT WE WERE ALREADY DOING (WHICH WAS EXTENDING INBOARD FLAPS WITH AN ALTERNATE SYS). BY LEAVING OUT A SECTION OF THE CHKLIST; I INADVERTENTLY MISSED AN IMPORTANT NOTE THAT STATED; 'DO NOT ATTEMPT TO MOVE FAULTY FLAPS BECAUSE THE ALTERNATE FLAP SYS HAS NO ASYMMETRY PROTECTION.' THE COMPANY HAS FOUND FAULT WITH US FOR NOT COMPLYING WITH THE ABNORMALS CHKLIST AND FOR NOT NOTICING THE FLAP MALFUNCTION UNTIL AFTER WE HAD EXCEEDED THE LIMITATIONS OF THE ACFT. THE INBOARD FLAP HYD MOTOR WAS FOUND TO HAVE FAILED SO IT WAS REPLACED AND A FLAP OVERSPD INSPECTION ON THE ACFT HAS BEEN ACCOMPLISHED AT THE CAPT'S REQUEST. THE CREW WILL PROBABLY HAVE SOME SORT OF ADDITIONAL TRAINING. I HAD NOT BEEN THROUGH TRAINING USING THE NEW ABNORMAL CHKLIST THAT WE CONSULTED; WHICH MAY HAVE AFFECTED MY PERFORMANCE. THE ABNORMAL CHKLIST DID NOT SEEM TO APPLY TO OUR PARTICULAR SIT EVEN THOUGH IT WAS THE PROPER CHKLIST; SO WE FOUND OURSELVES DISREGARDING A LOT OF THE ACTIONS; WHICH MAY HAVE CONTRIBUTED TO US MISSING THE CAUTIONARY NOTE. PUTTING CAUTIONARY NOTES AT THE BEGINNING OF A CHKLIST WOULD HAVE HELPED; AND A BETTER USE OF THE NORMAL CHKLIST BY THE CREW WOULD HAVE HELPED. SUPPLEMENTAL INFO FROM ACN 393691: ON TKOF WE WERE LOOKING RIGHT INTO THE EVENING SUN WHICH MAY HAVE BEEN A FACTOR IN MISSING THE LACK OF MOVEMENT OF THE TRAILING EDGE FLAP NEEDLES. ALSO THE OUTBOARD FLAP GAUGE IS THE TOP GAUGE NEXT TO THE LEADING EDGE FLAP LIGHT. THE OUTBOARD AND INBOARD FLAP NEEDLES USUALLY MOVE INSYNCH ON DIFFERENT GAUGES. THE POSSIBILITY EXISTS THAT OVER THE YRS THE LOWER INBOARD FLAP GAUGE HAS DROPPED OUT OF MY SCAN.