Date: 201603
Local time of day: 1801-2400
Location: DEN.Airport, CO
Flight conditions: IMC
Weather elements / visibility: Turbulence
Light: Night
Aircraft: Medium Large Transport; Low Wing; 2 Turbojet Eng
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Climb
Airspace: Class B DEN
ATC / advisory: TRACON D01
Reporter organization: Air Carrier
Reporter function: Captain; Pilot Not Flying
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Confusion; Situational Awareness
Second reporter function: Pilot Flying; First Officer
Anomaly: Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Person Flight Crew
When detected: In-flight
Result: Air Traffic Control Provided Assistance; Flight Crew Became Reoriented; Flight Crew Returned To Clearance
Contributing factors: Human Factors
Primary problem: Human Factors

Narrative: RNAV departure 34L. We got our clearance via PDC through ACARS. There was an amendment to the route and my FO plugged it in. It was minor by adding CHICI fix then DEHLI after YOKES. We taxied out to the west for the 34's. My FO had put in 34R for our dep runway. Traffic was moving pretty smoothly with quick departures going ground assigned us 34L and we taxied to the runway. After second engine start and taxi checklist completed we were about to Rwy 34L. As we were cleared to line up and wait we noticed our needle not centered and then realized 34R was still in. My FO changed runway to 34L and activated. We verified it was correct and the first fix on the YOKES was IRIIS and the remainder of the YOKES departure. At this time we were cleared for takeoff up to 10;000 RNAV to IRIIS. All was well on the departure then we were cleared to FL230. It was a typical light chop turbulence on the climb with IMC conditions. It was on the climb after IRIIS that ATC asked where we were heading. I was working the radios and told them KP78C fix. He asked if we'd been assigned that by previous ATC. We said no; at that time realizing that the other fixes had kicked out of the FMS navigation for some reason. He replied to us that this has been a frequent issue and then gave us a new direct to fix. It sounded like he gave us a fix that we'd had just passed by..CHICN..actually he gave us CHICI which was just a bit further down the departure. We both thought we heard him say the CHICN and not CHICI. It was a little confusing and were giving a higher altitude and a heading. I had mentioned to him (ATC) that it may have kicked out when we did a runway change right before departure. He again said it was happening quite often and that the departure would be changed effective [in a week]. He then gave us direct to our destination and then gave me a number to call when on the ground. I called and talked to the supervisor. He was nice and helpful and took my information. He also said the departure was changing and for some reason many issues with flight plans kicking out on this particular SID. That was the end of the day for myself and crew. No other issues happened after that.


Second narrative: [Report narrative contained no additional information.]


Synopsis: Before takeoff; flight crew received a late runway change to 34L at DEN. Reloading the FMS caused some amended waypoints to drop out of the flight plan which resulted in an incorrect track during climb out.