Custom Windows created in the editor or in flight aren't saving after closing kerbal space program
Edit: As well as after ending flights and starting new ones and when switching vessel

Are any other settings saving properly--for instance, the window positions of regular windows? Are you using MJ 2.0.4?

some of my ships on orbits don't get windows i've made and some do

I'm using 2.0.4 And I think most settings are saving but I have not tested very many of them. I've also added some extra info to my main post above

Should be really fixed this time, open it again if it happens again.