Hi HugeLunatic.
I've found that the original diagonal part of the Atomic Window on 2 tiles isn't slaved to the straight window and uses own subsets (as also happens with the straight and diagonal parts of other doors and windows). You can verify it if you want.
However I've already created a fix to this little problem, it's in the attached rar file. I've tested the package in the game and all works well now.
Take a look to the fix I've made and if you want you can add it to this mod (you can also rename the package).

Thanks for fixing, but please post issues with my content rather than attaching your fixes. I'll update with the diagonal when I get time to fiddle and test.

merci