During the last week or so, I am having the same problem. As an example, I can select (in the World section) to start at KROA, Parking Position 29, and all is well. Then I choose to fly to KHSP and all is well. Then I choose Low Altitude and then choose to change from DIRECT to SCUTA3 as my SID. Direct will fly you into a mountain if flying in a Cessna. The spot I selected earlier will change to a runway. This does not allow a cold and dark startup and is unrealistic. It also will not put the flight plan into the aircraft and has to be set up again inside the aircraft. It will sometimes, even then, require resetting the route since Working Title. I realize that the last part is a different subject (probably) but appears to be part of the whole problem.