MD80 FLT CREW LOSES TRANSITION WAYPOINTS ON NOBLY RNAV SID; LIT TRANSITION.

Narrative

WHILE FLYING THE NOBLY2 LIT TRANSITION DURING THE CLBOUT; THE FMS/AUTOPLT TRACKED DIRECT LIT AFTER TURNING AT THE NOBLY FIX. AFTER TAKING THE FUEL AND TIME I NOTICED THAT THE COBUG AND ORTRO FIXES WERE MISSING IN THE FMS. I WAS CHKING THE CHART AND IN THE PROCESS OF INPUTTING THE FIXES WHEN CTR CALLED AND ASKED IF WE WERE ON A HDG OR GOING DIRECT LIT. I SAID WE WERE HEADING TO LIT AND HE TOLD US TO TURN 10 DEGS R. AFTER THE TURN AND GETTING THE FIXES BACK IN I SAW THAT WE WERE TRACKING PARALLEL AND VERY CLOSE TO THE SID TRACK. WE DID VERIFY THE FLT PLAN AND SID AT THE GATE; ALL THE FIXES ON THE SID WERE PRESENT. AFTER TKOF I NOTICED THAT THE FMS WAS NOT DIRECTING THE FLT DIRECTOR TO THE TRACK CTRLINE AND I CORRECTED BY HAND FLYING TO THE TRACK. AFTER THE INITIAL TURN AND HEADING TO NAVYE THE FMS WAS TRACKING ON THE CTRLINE. THE ACARS PRINTER WAS INOP AND THE PNF IS EXTREMELY BUSY. AFTER COMPLETING THE TKOF/CLB CHKLIST; HE WAS WORKING THE FUEL/TIME DURING THIS PHASE. I BELIEVE THAT IF WE DID GET THE FLT PROGRESSION PLAN FROM THE ACARS; WE WOULD HAVE NOT BEEN DISTRACTED TO THE TIME THAT IT TOOK US TO SEE THE PROBLEM.