Also note that both the glare shield above the window and the window itself are both loaded correctly.

I'm very confused that this has happened. While I've had this happen before with other aircraft, a Captain Sim aircraft has never done this (Weapon has not done it either). I guess the 707 is just really complicated or something (though I'm not sure if it's complexity tat does it, seeing as one aircraft that I had was not very complex, just a simple private jet, and it caused the same problem).