AFTER BEING CLRED TO FL290 THE PNF; VERIFIED BY THE PF; PUT FL290 IN THE ALT ALERT WINDOW. SUBSEQUENTLY; AS THE ACFT WAS CLBING THROUGH FL290 THE PNF NOTICED FL310 WAS IN THE ALT ALERTER. NEITHER THE PF NOR THE PNF HAD CHANGED THE SETTING OF FL290. THE FLT CTLR; WHEN ASKED BY THE PF; CONFIRMED THEY WERE STILL CLRED TO FL290. A 600 FT ALT EXCURSION OCCURRED IN THE PROCESS OF THE PNF GETTING THE ACFT LEVELED AT FL290. THE ACFT HAD A NUMBER OF FLT GUIDANCE SYS DISCREPANCIES.

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AFTER DEPARTING SEA ARPT AND BEING HANDED OVER TO ZSE; THE ACFT WAS CLRED TO FL290; I; AS THE PNF; PUT FL290 IN THE ALT ALERT WINDOW. I THEN ADVISED THE PF THAT I WAS LEAVING THE FREQ TO CALL IN OUR DEP TIME TO OUR COMPANY OPS; AFTER HE CONFIRMED OUR ALT CLRNC OF FL290. AFTER CALLING IN THE DEP TIME AND RETURNING TO THE FREQ; I LOOKED UP AT THE INST PANEL AND SAW THAT THE ACFT WAS ABOUT TO PENETRATE FL290 AND THAT 31000 FT WAS NOW SET IN THE ALT ALERT WINDOW. I ASKED THE PF IF THERE WAS A CHANGE IN OUR ALT CLRNC AND HE INFORMED ME THAT THERE WAS NOT. I IMMEDIATELY DISCONNECTED BOTH THE AUTOPLT AND THE AUTOTHROTTLES. I REDUCED THE PWR AND PUSHED THE NOSE OVER TO HOLD THE ALT AT FL290. WE PENETRATED OUR ALT OF FL290 BY APPROX 600 FT. WHILE I WAS DOING THIS; THE FO ASKED ATC WHAT OUR ASSIGNED ALT WAS. ATC STATED IT AS BEING FL290. THE FO (PF) INFORMED ME THAT HE NEVER PUT 31000 FT IN THE ALT ALERT WINDOW. WE BOTH VERIFIED FL290 WHEN IT WAS INSERTED IN THE ALT ALERT WINDOW. THE ACFT HAD A NUMBER OF ADDITIONAL DFGS MISHAPS DURING THE FLT. THIS SYS CTLS THE AUTOMATION OF THE ACFT. I WOULD ALSO LIKE TO STATE THAT ON PREVIOUS OCCASIONS I HAVE OBSERVED THAT A DIGIT (WHICH IS NOTHING MORE THAN A LIGHT) SET ON THE DFGS PANEL HAS CHANGED TO A HIGHER OR LOWER NUMBER FOR NO APPARENT REASON.