AN UNEXPLAINED CHANGE IN THE FMS RTE LOADING LEADS TO A TRACK DEV.

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THIS IS A NEW ACFT TO ME BUT A SIMILAR TYPE AND THE AVIONICS AND FMS ARE FAMILIAR TO ME. MY COPLT IS NEWLY TYPE RATED IN THIS ACFT AND UNFAMILIAR WITH THE FMS. I REVIEWED THE PROC FOR LNDG WITH THE PF AND INITIALIZING USING THE PWR SAVE MODE OF THE FMS WITH THE COPLT. WE WERE USING A GPU SINCE THIS ACFT DOES NOT HAVE AN ONBOARD APU. I WATCHED THE COPLT ENTER THE FLT PLAN AND INITIALIZE THE FMS CONFIRMING THAT EVERYTHING WE PROGRAMMED WOULD BE SAVED DURING START UP WITH THE PWR SAVE MODE ON. AFTER PERFORMING THE REST OF THE PRE-START CHKS; I LEFT THE COPLT TO COPY ATIS AND CLRNC. I RETURNED WITH THE PAX AND CONTINUED WITH STARTING ENGS. (NOTE THAT THIS ACFT IS STARTED WITH THE AVIONICS OFF WHICH IS WHY IT IS IMPORTANT TO USE THE PWR SAVE MODE TO RETAIN FMS PROGRAMMING.) AS WE BEGAN OUR AFTER START CHKS I ASKED THE COPLT IF WE WERE CLRED AS FILED AND THE FLT PLAN WAS STILL IN THE FMS. SHE REPLIED IN THE AFFIRMATIVE AND I GLANCED DOWN AT THE FMS TO CONTINUE. THE FLT PLAN WAS UP ON THE FMS AND I FELT COMFORTABLE SINCE I HAD CONFIRMED THE FLT PLAN ENTRY AND THE FMS DID NOT COME UP ON THE IDENT PAGE (WHICH IT WOULD HAVE DONE WERE THE PROGRAMMING AND INITIALIZATION NOT SAVED). I COULD CONFIRM THE FIRST FIX WAS CORRECT FROM MY PFD AND MFD DISPLAY BUT DID NOT NOTICE THAT THE SECOND FIX WAS HNK INSTEAD OF SYR. SHORTLY AFTER GOING FROM MHT TO HNK CTR QUESTIONED OUR ROUTING. I THEN LOOKED AT THE FMS AND SAW THAT EVERYTHING WAS DIFFERENT (INCORRECT) AFTER MHT. AFTER VERIFYING OUR CLRNC WITH CTR WE PROCEEDED DIRECT SYR. I REVIEWED THE FLT PLAN IN THE FMS AND COMPARED IT AGAINST OUR COMPUTER FLT PLAN (PAPER) AND THE CLRNC. EXCEPT FOR THE FIRST FIX THE FLT PLAN IN THE FMS DID NOT RESEMBLE OUR FILED PLAN ON CLRNC. I WAS PUZZLED AS TO HOW THESE WAYPOINTS WERE PROGRAMMED WHEN WE HAD NOTHING IN THE COCKPIT THAT REFLECTED SUCH A ROUTING AND I HAD VERIFIED THE ENTRY EARLIER WITH THE COMPUTER FLT PLAN SHEET. I REMEMBERED THAT I HAD FLOWN THIS RTE THE PREVIOUS WK AND CHKED TO SEE IF THERE WAS A FLT PLAN SAVED IN THE FLT PLAN LIST; THERE WAS AND IT CONTAINED THE INCORRECT ROUTING. SOMEHOW THIS FLT PLAN HAD BEEN SELECTED AND ACTIVATED FROM THE FLT PLAN LIST AFTER THE CORRECT FLT PLAN HAD BEEN ENTERED. I QUESTIONED THE COPLT BUT SHE SAID SHE 'HAD NOT TOUCHED IT.' I CAN ONLY ASSUME THAT THE COPLT HAD CONTINUED HER FMS EDUCATION AFTER I DEPARTED THE ACFT AND HAD SELECTED AND ACTIVATED THE 'OLD' FLT PLAN FROM THE FLT PLAN LIST. I SHOULD HAVE REVIEWED THE ROUTING ENTERED IN THE FMS MORE THOROUGHLY AFTER START UP. ALSO I SHOULD HAVE VERIFIED THE NEXT FIX OVER MHT WHEN A TRACT CHANGE WAS EVIDENT. THE COPLT SHOULD BE COMMANDED TO FOLLOW THE RTE EITHER WITH THE SECOND FMS ON VOR AS APPROPRIATE. SHE WAS TUNED TO THE LAST VOR AND NOT PROPERLY SET FOR OUR RTE OF FLT.