Some waypoints in the sets of flight plans are jus positions recorded on the flight plan are not recognized by the flight sim as valid locations. If you refer to the tour documentation, (the flight legs details section of the pdf), you'll see references stating "SAVE POSITION" on some of the flight legs - which means save the flight in the sim (which also saves your aircraft position).
So these end points that are not recognized as a start point in the sim, your sim can't just load them as a start position. THe only way to get there is either by lat/long of that location or the position is saved in the flight.
So if you have saved your flight when you end at those points, your aircraft position is also saved so when you start the next leg, your aircraft will be a the correct/saved position to start that leg.