Medium Large Transport; Low Wing; 2 Turbojet Eng
Flight Crew Air Transport Pilot (ATP)
Human-Machine Interface; Situational Awareness
Aircraft Equipment Problem Less Severe; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Inflight Event / Encounter CFTT / CFIT
Air Traffic Control Issued Advisory / Alert; Air Traffic Control Issued New Clearance; Flight Crew Became Reoriented; Flight Crew Returned To Clearance
Aircraft; Human Factors
We had some issues with the FMS before Departure while preflighting the aircraft and I thought we had corrected the issues and the FLIGHT PLAN/LEGS were verified.   For some reason; my side (Captains) did not load the departure runway and the fix JAPER and instead NAVIGATED my FMS to direct BOBKT which caused the course deviation.  Also; as a note the EGPWS TERRAIN went completely RED right after takeoff which we commented that it seemed to not be correct.  The Traffic (TFC) was in the 5 mile range which should have given us some green/yellow/red. This problem added to the workload because our TERRAIN MAP appeared to be not working.After TAKEOFF from BZN RWY 12; I asked for NAV mode at 400 foot to follow the BOBKT2 loaded in the FMS.  After contacting BIG SKY APPROACH they asked us if we were OFF COURSE.  We then noticed that even though the FMS were synched my FMS had not picked up the first FIX-JAPER and instead we were direct BOBKT.  They gave us an ALTITUDE ALERT MVA of 10;900 on the direct BOBKT heading.  We asked for RADAR VECTORS and BIG SKY Departure gave us a heading of 130.  They gave us an ALTITUDE ALERT MVA of 10;900 on the direct BOBKT heading.  We switched the FMS to FMS 2 which had the correct departure procedure.  We were both in Terrain Mode which appeared to be giving us erroneous information as we were climbing.  This information added to the workload.  We never received any TERRAIN alerts. We continued the climb at a max rate while maneuvering to get back on the proper SID. After clearing the SID BOBKT2 departure BIG SKY asked us to call them after landing.  I called them and discussed the FMS/NAVIGATION problems we had with the Quality Control Supervisor and Station Chief.AUTOMATION errors caused the issue. We had followed SOP procedures and verified the legs before TAKEOFF. I cannot say why my side FMS did not pick up the runway and the proper NAVAIDs.  When I select TOGA it should GPS position us.  RWY 12 was selected.  My suggestion is that since this situation can occur and it is apparent that the FMS can cause errors; would be to overlay critical FIX(s) with the FIX(s) page.  Verify that our FMS(S) match.  I am not sure what happened with the EGPWS/TERRAIN but that was very disconcerting.  We were in an extremely high workload situation while we were trying to follow the climb profile/flaps retraction and determine what was wrong.   My suggestion(s) would be to: 1) ask for Radar vectors to the appropriate fixes. 2) NEXT; verify the course. 3) RELOAD the FIX(s) if necessary.  4) In this case: The FMS (2) was correct the pilots should select the proper course info on the flying pilot side.  5) Switch controls if needed.  6) Look at the Fix Page to make sure you are meeting the SID profile.  All this is high workload while under stress trying to determine what is the problem.   If possible RADAR VECTORS should be the first request while the pilots determine what is the problem; or ask for a climb away from the TERRAIN THREAT.As a further suggestion; the FAA should look at this departure because of the possible FMS/NAVIGATION errors and make changes. The BOBKT2 navigation for RWY12 climbs the aircraft through a valley between two mountain ranges.  It would be safer to turn aircraft right after departure to a 300 heading and climb to a safe altitude before turning eastbound over the mountains.  I think lost navigation procedures while climbing should include this to keep aircraft clear of the mountains.
Called to verify that the two FMSs are not automatically synced in this aircraft. The reporter verified that they are not.
An aircraft FMS did not have the departure runway loaded on the pilot flying's side. It was verified via callback that the two FMSs do not automatically sync in this aircraft. After takeoff the aircraft directed navigation to the wrong fix; resulting in ATC issuing an altitude alert.