You also need to remove the back canopy from the area where you build the planes. And select it again from the left side where all the parts are in the SPH (spaceplane hangar). This is because the craft files may save the incorrect node position. I previously had a problem with the download from kerbal.net and it gave out a wrong version, it is now working however. Your problem simply should not happen if you deleted the parts, and delete the canopy in the sph once. Make sure you don't have other KSP copies you might be using, and that the shortcut you press to start the game is referring to that folder where you made the changes. I'm sorry but this is all I can do for you. // --- node definitions --- // definition format is Position X, Position Y, Position Z, Up X, Up Y, Up Z node_stack_top = 0.0, -4.94409, 10.0054, 0.0, -1.0, 0.0, 0