Falcon 900
Flight Crew Flight Instructor
Flight Crew Last 90 Days 36; Flight Crew Total 7000; Flight Crew Type 465
Communication Breakdown; Confusion; Human-Machine Interface
Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Air Traffic Control Issued New Clearance; Flight Crew Became Reoriented
Human Factors; Manuals
While on the RODIO2 RNAV Arrival into San Antonio (KSAT); the ATIS informed us Runway 4 was in use. The Pilot Flying entered the Runway and ILS 04 in the FMS while I checked the chart.  While comparing the waypoints he mentioned that the FMS had us going over TROOP and CRISS intersections. At first glance I thought runway 4 would take us over the southern arrival gate using POYIG and BERNE; then saw the note at CRISS that listed Runways 4; 12R; 30L so I agreed we would be using CRISS.  Shortly; the approach controller asked if we were on the RWY 4 arrival course and I confirmed we were and expecting RWY 4. He came back in a minute and gave us a heading.  I thought that might mean we were on the wrong one so I checked again and noticed that the note at CRISS stated 'LANDING OTHER THAN SAN ANTONIO INT'L RWYS 4; 12R; 30L'. I asked if we should rejoin and we were cleared to.Then we had to resolve why the FMS had kept the wrong transition points. We don't know exactly but I found that to get the correct ones I not only had to enter the RWY and APPROACH but if I selected the STAR that it changed the waypoints to the correct transition.  It is now my conclusion that when the flight plan was filed; the RODIO2 was filed without a runway; but the CRISS arrival transition was in the flight plan. We were cleared as filed so these remained in the flight plan as it was loaded in the FMS.  The waypoints were correct but the RODIO2 was not in the FMS as a STAR; merely as waypoints that were chosen from the flight planning software for filing.My mistake was obvious (misreading the note) but aggravated and allowed by the FMS issue which caused me to believe my mistake.  I would think that avoiding words like 'OTHER THAN' would avoid missing this negative reference to the runways that are NOT intended.
A flight crew discovered that their FMS had kept the wrong transition points for their arrival runway. The arrival STAR was not loaded in the FMS. A confusing note over an expected transition point added to the confusion.