FLT CREW OF C560 HAD TO OVERRIDE AUTOFLT SYS WHEN THE ACFT DIVERTED FROM TRACK. DURING RECOVERY; ALT DEVIATED 300 FT FROM ASSIGNED.

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WHEN APCHING CRAYS INTXN ON THE MARCS 7 ARR INTO SAT; THE AUTOPLT (WHILE UTILIZING FMS NAV GUIDANCE) COMMANDED A TURN TO THE L RATHER THAN PROCEEDING TO THE NEXT FIX ON THE ARR WHICH WOULD HAVE BEEN MARCS INTXN. SEEING THAT THE ACFT WAS TURNING AWAY FROM THE CORRECT COURSE; I INSTRUCTED THE FO; WHO WAS PF; TO SELECT HDG MODE AND MAKE AN IMMEDIATE COURSE CORRECTION. THE FO THEN DISCONNECTED THE AUTOPLT AND THE ACFT IMMEDIATELY LOST 300 FT OF ALT AND TURNED MORE RAPIDLY TO THE L. I BRIEFLY ASSUMED CTL OF THE ACFT AND MADE AN IMMEDIATE ALT CORRECTION AND BEGAN A TURN BACK TOWARD THE CORRECT COURSE. I RETURNED THE CTLS TO THE FO; THE AUTOPLT WAS RE-ENGAGED. ATC STATED 'YOU ARE S OF COURSE; FLY HDG 290 DEGS.' HDG 290 DEGS WAS SELECTED AND THE ACFT WAS RE-ESTABLISHED ON THE PROPER COURSE FOR THE ARR. THERE WAS NO FURTHER COM FROM ATC REGARDING THE MATTER. IT APPEARS THE ACFT WAS ATTEMPTING TO ENTER A HOLDING PATTERN AT CRAYS FOR REASONS UNKNOWN. THIS SIT COULD HAVE BEEN PREVENTED BY ASSUMING CTL OF THE ACFT SOONER AFTER MAKING REPEATED STATEMENTS TO THE PF TO MAKE A COURSE CORRECTION. I STILL DO NOT KNOW WHY THE FMS WOULD COMMAND THE AUTOPLT TO ENTER HOLDING WHEN NO HOLDING PATTERN HAD BEEN PROGRAMMED.